Alignments for a candidate for ofo in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Herbaspirillum autotrophicum IAM 14942

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_083439286.1 AKL27_RS24935 indolepyruvate ferredoxin oxidoreductase

Query= reanno::Cup4G11:RR42_RS19540
         (1197 letters)



>NCBI__GCF_001189915.1:WP_083439286.1
          Length = 1175

 Score = 1083 bits (2801), Expect = 0.0
 Identities = 588/1177 (49%), Positives = 754/1177 (64%), Gaps = 42/1177 (3%)

Query: 24   DKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWKAKQ 83
            + Y  E GR+Y++GTQALVRLP++QR  DR  GL+TAG ISGYRGSPLG  DQ LWKA  
Sbjct: 21   EMYGRESGRIYLTGTQALVRLPLMQRRLDRLHGLHTAGLISGYRGSPLGTYDQQLWKASA 80

Query: 84   HLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVFKHA 143
            HLAAHDIVFQ GLNEDLAAT++WG+Q    + +   +GVFG+WYGKGPGVDR+ DV + A
Sbjct: 81   HLAAHDIVFQPGLNEDLAATALWGAQMHKAFGEVTADGVFGIWYGKGPGVDRSGDVLRAA 140

Query: 144  NSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHAWAM 203
            N  G+S  GGVL ++GDDHAA+SS   HQ++ IF++  +P+L P+N++E L +GL   AM
Sbjct: 141  NMLGTSALGGVLAVSGDDHAAQSSMYPHQTDGIFQSASIPILQPANLEEILAFGLAGIAM 200

Query: 204  SRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLN----IRWPDPPLEQ 259
            SR+SGLWV +K + +V+E++ S++L P     V P DFI+P  GLN    I WP    E 
Sbjct: 201  SRFSGLWVCLKTIAEVIETAGSLQL-PETPVYVTPSDFIVPAHGLNWDPRIAWPGQRAEL 259

Query: 260  EARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCA 319
            E RLL  +  A LA+ RAN IDR  +   +AR GI+T GKA+ D  QA+ +LGL      
Sbjct: 260  ERRLLAERLPAALAWARANGIDREVVPGANARLGIVTVGKAHQDVMQAIRDLGLSHADLQ 319

Query: 320  RIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVY 379
             +GI +YKVG  WPLE  G R FA G +E+LVVEEKR I+E  +K+ LY+    VR +V 
Sbjct: 320  ALGIAIYKVGMSWPLETVGMRRFAAGKEELLVVEEKRAIVESQIKDALYHSDATVRTRVV 379

Query: 380  GKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAARIAV 439
            GK D+               LLP   E +P ++A+ +  R+ +   PA     + AR+  
Sbjct: 380  GKTDQHGAP-----------LLPEISEFNPLLLAQVLLARIGE-RAPA-----LKARLQA 422

Query: 440  IEAKEKAMAVPRVAAE-RKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWM-DRSTST 497
            ++A         VA   R+P+FC+GCPHNTST  P+GS +  GIGCH M +   +  TST
Sbjct: 423  LQAAASGGFRSDVATPVRRPYFCAGCPHNTSTKSPDGSVSGGGIGCHVMALTEPELKTST 482

Query: 498  FSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAV 557
            FSQMGGEG  WIG APF+  +HVF NLGDGTY HSGLLAIRA++AA  N+TYKILYNDAV
Sbjct: 483  FSQMGGEGAQWIGAAPFSATRHVFQNLGDGTYQHSGLLAIRAALAAKTNVTYKILYNDAV 542

Query: 558  AMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRI 617
            AMTGGQP +G++    +  Q+ AEG   I +V+D+P+++    +L   V VHHRD++D++
Sbjct: 543  AMTGGQPAEGQIDPARITRQLHAEGVSTIALVSDQPQRWQGNAELAANVVVHHRDQMDQV 602

Query: 618  QRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLS 677
            QRE+REVPG T +IY+QTCA+EKRRRRKR  YPDP KR FIN  VCEGCGDCSV+SNC++
Sbjct: 603  QREMREVPGVTAIIYEQTCASEKRRRRKRKEYPDPDKRLFINPRVCEGCGDCSVQSNCIA 662

Query: 678  VEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPE---RHGVSMDNLPAL 734
            V+PLET  G KR INQS+CNKDFSCV GFCPSFV  +G Q++KP+      +  D L  L
Sbjct: 663  VQPLETAFGRKRVINQSACNKDFSCVKGFCPSFVEIDGVQLRKPDAARMKTIEADALAQL 722

Query: 735  PQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSH 794
            P  ++    H Y + +TG+GGTGV+T+G LLG AAHLENKG +VLD  GLAQK GAV+S 
Sbjct: 723  PPASMALPAHAYNIYITGIGGTGVLTLGALLGAAAHLENKGASVLDFTGLAQKNGAVVSQ 782

Query: 795  VQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFI 854
            V+IAA PD++ A RI +G  DL+IG D +V+A  D + +    RT AIVN  QTPTA+ +
Sbjct: 783  VRIAASPDEIDAVRIGIGAVDLLIGTDLVVAAGADNLLRLAATRTTAIVNLDQTPTADVV 842

Query: 855  KNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLS 914
                   P + A  D            NAS LA  L GD +  + L+LGYAWQ+G +PLS
Sbjct: 843  TQRDATLP-VDAMLDSVQRNSSVMHTFNASTLAQQLFGDTVAAHTLMLGYAWQRGLVPLS 901

Query: 915  LDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGA 974
            L AL RAIELNG A+E NK A  WGR  A  P  +  L G+  +    A     P + G 
Sbjct: 902  LAALERAIELNGAAIEMNKRALSWGRIAAASPATLALLDGEAASVNAPA-----PKNFGD 956

Query: 975  LLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLM 1034
             L     H  + L AYQD AYAQ +R    R R AE A+ G+        A AR   KLM
Sbjct: 957  AL----MHFQQELVAYQDTAYAQRYRQLAMRARQAEQAVAGSVDDGAFALAVARQAYKLM 1012

Query: 1035 AYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRD-EKGHLVKRRFG 1093
            AYKDEYEVARLY  P F   L  QF         +  WLAPPL+++ D   G   KR+FG
Sbjct: 1013 AYKDEYEVARLYAAPEFKAALMQQFSVAS----NIGIWLAPPLLSRIDAATGRPRKRKFG 1068

Query: 1094 PSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAI 1153
            P  +  F VLAKL+GLRG  FD FG+T ERR ER L+ +Y A+++ L  GL+  N A A 
Sbjct: 1069 PWVLSAFKVLAKLRGLRGSRFDPFGRTEERRLERQLVTDYFAMIDTLCAGLNRDNLAVAT 1128

Query: 1154 TLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHP 1190
             LA+LP  +RG+G VK   +     +   LL +F  P
Sbjct: 1129 ELAALPAMVRGYGPVKLAAIKDYEQQKALLLTRFAKP 1165


Lambda     K      H
   0.319    0.135    0.407 

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: 3120
Number of extensions: 123
Number of successful extensions: 10
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: 1197
Length of database: 1175
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1128
Effective search space:  1297200
Effective search space used:  1297200
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: 59 (27.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources