GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adiA in Shewanella loihica PV-4

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 5209141 Shew_1619 arginine decarboxylase (RefSeq)

Query= BRENDA::Q7MK24
         (640 letters)



>FitnessBrowser__PV4:5209141
          Length = 637

 Score =  873 bits (2255), Expect = 0.0
 Identities = 426/624 (68%), Positives = 513/624 (82%), Gaps = 1/624 (0%)

Query: 18  YNVHYWSQGFYGIDDQGEMYVSPRSDNA-HQIQLSKIVKQLEERQLNVPVLVRFPQILHQ 76
           YNV+YWS G YGI + GE+ VSP  ++  H I L+++ K + +  + +PVLVRFPQILH 
Sbjct: 13  YNVNYWSSGLYGISEAGEVTVSPDPNHPEHTIGLNELAKDMVKSGVALPVLVRFPQILHH 72

Query: 77  RVHSICDAFNQAIEEYQYPNKYLLVYPIKVNQQREVVDEILASQAQLETKQLGLEAGSKP 136
           RV+S+C+AFNQAI  Y Y + YLLVYPIKVNQQ+ VV+EILASQ   E  QLGLEAGSKP
Sbjct: 73  RVNSLCNAFNQAITRYDYQSDYLLVYPIKVNQQQTVVEEILASQVSKEVPQLGLEAGSKP 132

Query: 137 ELLAVLAMAQHASSVIVCNGYKDREYIRLALIGEKLGHKVFIVLEKMSELDLVLREAKSL 196
           EL+AVLAMAQ ASSVI+CNGYKD EYIRLALIGEKLGH+V+IVLEK+SEL +VL EAK L
Sbjct: 133 ELMAVLAMAQKASSVIICNGYKDVEYIRLALIGEKLGHQVYIVLEKLSELKVVLEEAKKL 192

Query: 197 GVTPRLGIRIRLASQGAGKWQASGGEKSKFGLSASQVLNVISRLKKENQLDTLQLVHFHL 256
           GVTPRLG+R+RLA QG GKWQASGGEKSKFGLSA+QVLNVI+ LK E+ LD+LQL+HFHL
Sbjct: 193 GVTPRLGLRVRLAFQGKGKWQASGGEKSKFGLSAAQVLNVINSLKDEDMLDSLQLLHFHL 252

Query: 257 GSQMANIRDVRNGVNESARFYCELRTLGANITYFDVGGGLAIDYDGTRSQSSNSMNYGLV 316
           GSQ+ANIRD+R+GV+E+ RFYCEL+ +GAN+  FDVGGGLA+DYDGTRSQSSNSMNYGL 
Sbjct: 253 GSQIANIRDIRSGVSEAGRFYCELQKMGANVKCFDVGGGLAVDYDGTRSQSSNSMNYGLT 312

Query: 317 EYARNIVNTVGDVCKDYKQPMPVIISESGRSLTAHHAVLISNVIGTETYKPETVTEPEED 376
           EYA NIV+ + D+C+++ QPMP +ISESGR LTAHHAVLI++VIGTE YKPE +  P+E+
Sbjct: 313 EYANNIVSVLNDMCREHDQPMPRLISESGRYLTAHHAVLITDVIGTEAYKPEDLQAPDEE 372

Query: 377 FPLLLNNMWRSWLNLHNGTDARALIEIYNDTQSDLAEVHSQFATGVLTLEHRAWAEQTSL 436
            P  L NMW SW  +    D RALIEIY+D QSDLAEVHS FA G ++L  RAWAEQ +L
Sbjct: 373 APQQLKNMWDSWGEVSGRADQRALIEIYHDVQSDLAEVHSLFALGQMSLSDRAWAEQMNL 432

Query: 437 RIYYELNRLMSTKNRFHRPILDELSERLADKFFVNFSLFQSLPDSWGIDQVFPVLPLSGL 496
           R+ YEL  +MS K RFHRP++DEL+E+LADKFFVNFSLFQSLPD+WGIDQVFPV+PLSGL
Sbjct: 433 RVCYELKGVMSGKYRFHRPVIDELNEKLADKFFVNFSLFQSLPDAWGIDQVFPVMPLSGL 492

Query: 497 QNAADRRAVMLDITCDSDGAIDAYVDGQGIESTLPVPAWNEDEPYLMGFFLVGAYQEILG 556
               +RRAVMLDITCDSDG +D YVDGQGIE+TLPVPAW+ + PYL+GFFLVGAYQEILG
Sbjct: 493 DKKPERRAVMLDITCDSDGTVDQYVDGQGIETTLPVPAWSAESPYLIGFFLVGAYQEILG 552

Query: 557 DMHNLFGDTHSVVVNVGDQGEINIDFINEGDTVEDMMRYVHIDVDQIRKNYHSLVSQRVD 616
           DMHNLFGDT+S VV + D G +NI+ +  GDTV D++RYV++D     + Y  LV+  + 
Sbjct: 553 DMHNLFGDTNSAVVRLDDDGLVNIESVLAGDTVADVLRYVNLDAVSFMRTYEELVNLHIQ 612

Query: 617 QEEQQQILAELEQGLSGYTYLEDF 640
           ++E+  IL EL+ GL GYTYLEDF
Sbjct: 613 EDERANILEELQIGLKGYTYLEDF 636


Lambda     K      H
   0.318    0.135    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1191
Number of extensions: 49
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 640
Length of database: 637
Length adjustment: 38
Effective length of query: 602
Effective length of database: 599
Effective search space:   360598
Effective search space used:   360598
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 5209141 Shew_1619 (arginine decarboxylase (RefSeq))
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.7918.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7918.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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