RPSBLAST alignment for GI: 254780611 and conserved domain: TIGR02394

>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). Length = 285
 Score =  134 bits (338), Expect = 4e-32
 Identities = 84/279 (30%), Positives = 139/279 (49%), Gaps = 29/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  A   ++ S+LRLVV IA  Y   GLP+ ++
Sbjct: 18  YLREIGFKPLLTAEEEIAYARRALA-GDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 77  IEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHV-IKELNVY 135

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L+         E++          +++ L ++E  + S++  L  D S + L 
Sbjct: 136 LRAAR-QLEKKLGREPSVEEIAELLDKPVEDVSRVLALNER-ITSLDAPLDDDSSKSLLD 193

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RL 248
             +D+                E ++   + ++     L      LN R+R +   R   L
Sbjct: 194 TIADEQ-----------SIDPESLVQNDDLKQLIEAWLAE----LNERQREVLARRFGLL 238

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE +++E  ++RERVRQI+  A KK++  +++ 
Sbjct: 239 GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERD 277