Alignments for a candidate for iorA in Desulfarculus baarsii DSM 2075

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Desulfarculus baarsii DSM 2075

Align Indolepyruvate oxidoreductase subunit IorA; IOR; Indolepyruvate ferredoxin oxidoreductase subunit alpha; EC 1.2.7.8 (characterized)
to candidate WP_013258571.1 DEBA_RS08765 indolepyruvate ferredoxin oxidoreductase subunit alpha

Query= SwissProt::P80910
         (618 letters)



>NCBI__GCF_000143965.1:WP_013258571.1
          Length = 632

 Score =  531 bits (1368), Expect = e-155
 Identities = 290/638 (45%), Positives = 400/638 (62%), Gaps = 36/638 (5%)

Query: 3   LDDILDAGRGDRLFLLGNEAAVRAAIESGVGVASTYPGTPSSEIGNVLSKIAKRAG---- 58
           +DD+L    G +  LLGNEA VR A+E+G+  A+ YPGTPSSE+ + L ++ +++     
Sbjct: 1   MDDLLSPKGGAQKLLLGNEAIVRGALEAGLAFATCYPGTPSSEVPDTLHRLMRQSPEQVK 60

Query: 59  IYFEFSINEKVALEVAAAAAASGVRSFTFMKHVGLNVASDSFMSVAYTGVRAGMVVLSAD 118
            +FE+S NEKVALE A+ AAA+G+R+   MKHVGLNVA+D  M++AY+GVRAGMV+L+AD
Sbjct: 61  YHFEYSTNEKVALETASGAAAAGLRTLCTMKHVGLNVAADPLMTLAYSGVRAGMVILTAD 120

Query: 119 DPSMFSSQNEQDNRHYARLAWVPLLEPSNPQEILEYMNHAFELSEEYRIPVLLRTTTRVS 178
           DPS+FSSQNEQDNR+YAR + +P+LEP++P +      +A ELSE+   PVLLRTTTRV+
Sbjct: 121 DPSLFSSQNEQDNRYYARQSGLPMLEPADPAQAKAMTKYAMELSEQLETPVLLRTTTRVN 180

Query: 179 HMRGVVEAGERRAEPVKGFFRKNPEQFVPVPATARVMRRELVEKMKKLKRVADTSELNRV 238
           H RG V   +      K  F K P +FV VPA +R +   L+   +K + +++ S  N V
Sbjct: 181 HTRGAVGLDDLPEVKTKAHFVKEPTRFVGVPAVSRNLHLRLLRIYEKAQALSEASPFNSV 240

Query: 239 LNEDSESDLGIIASGGAFNYVYDALQTLGL--DVPVLKLGFTYPFPAGLVAEFLSGLEGV 296
                +  LG++A G    YV DA++ L     + +  LGF++P P   +A FL  ++ V
Sbjct: 241 ---KGKGRLGVVACGVCVAYVADAVKDLDAAGQIKIFNLGFSWPLPEKKLARFLKSVDQV 297

Query: 297 LVVEEVDSVMEKEVLAVATSEGLDVGVHGKLDGTLPEI-------------YEYSEDIVR 343
           LVVEE++ ++E  + A+A  +G+ V + GK  G +P +             YEY+  +VR
Sbjct: 298 LVVEELEPLVENALRAIAQEKGIAVKISGKTPGAIPAVSVDVRAPEVFTRAYEYNPRLVR 357

Query: 344 RAISGLTGIKSHEKGI----EAPELPERPPALCPGCPHRAMYYSVRRAASELGIEGEDLI 399
           + I+    +K +   +    + P LP RPP LC GCPHRA Y++V++A       G + +
Sbjct: 358 QTIAKAFKLKDNSPPVLDLSDRPALPGRPPNLCAGCPHRATYFAVKQAV------GPEAV 411

Query: 400 FPTDIGCYTLGIEPPYSAADYLLSMGSSVGTACGFSAATSQRIVSFIGDSTFFHAGIPPL 459
           F TDIGCYTLG+ PP S ADYL+ MGSSV +A G + AT Q++V+FIGDSTFFH+GI  L
Sbjct: 412 FTTDIGCYTLGMLPPISMADYLICMGSSVSSAGGIARATDQKVVAFIGDSTFFHSGITGL 471

Query: 460 INAVHNRQRFVLVILDNRTTAMTGGQPHPGLPVDGMGEEAPAISIEDITRACGVEFVETV 519
           +NAVHNR  F LVILDN TTAMTG QPHPG+   G+ ++   + IE + R  GVE V TV
Sbjct: 472 VNAVHNRHNFTLVILDNGTTAMTGHQPHPGVS-QGLADDKTHVDIEKLVRGLGVEHVTTV 530

Query: 520 NPMNIRRSSETIRRALQHESVAVVISRYPCML--SEGAVRGR-PVRVDEEKCDLCLECLN 576
            P  +  S + I+ A  +  V+VVISR  C L     A RGR P RVD  KC    +C+N
Sbjct: 531 KPFKVAASVKAIKEAADYPGVSVVISREICPLYGRRVAPRGRKPFRVDPGKCKNHRDCIN 590

Query: 577 ELACPAIVEEDGRVFIDPLYCRGCTICLQICPAGAIKP 614
            +ACPA      +  I+   C GC +C QICP  AI P
Sbjct: 591 TVACPAFYIAGDQPAINASQCIGCALCAQICPENAITP 628


Lambda     K      H
   0.319    0.137    0.398 

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: 893
Number of extensions: 35
Number of successful extensions: 8
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: 618
Length of database: 632
Length adjustment: 37
Effective length of query: 581
Effective length of database: 595
Effective search space:   345695
Effective search space used:   345695
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)

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

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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