Alignments for a candidate for iorA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Dechlorosoma suillum PS

Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate Dsui_0095 Dsui_0095 indolepyruvate ferredoxin oxidreductase, alpha/beta subunit

Query= BRENDA::Q6LZB6
         (578 letters)



>FitnessBrowser__PS:Dsui_0095
          Length = 621

 Score =  501 bits (1289), Expect = e-146
 Identities = 269/596 (45%), Positives = 382/596 (64%), Gaps = 27/596 (4%)

Query: 4   LMLGNEAVARGAYEAGVLVATAYPGTPSTEITEHISKYPEINSEWSVNEKVALEVAIGSA 63
           LM GNEAVAR  +EAGV VA AYPGTP+TE+ E IS YP++ +EWSVNEKV+LEVA+G+A
Sbjct: 14  LMSGNEAVARAVWEAGVKVAAAYPGTPATEMLEVISTYPDLYAEWSVNEKVSLEVAVGAA 73

Query: 64  IAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLIIVADDPSMHSSQNEQDTRYYGIFS 123
            AG+R+   MKHVG+NVA+D LMT+  TG+  GL+I VADD  + SSQNEQD+RY+G F+
Sbjct: 74  YAGSRSFCCMKHVGMNVASDALMTLTLTGVAGGLVIAVADDVGLSSSQNEQDSRYWGRFA 133

Query: 124 KIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLVELEEKEKIELKPYD 183
            +PVLEP+DSQE  +  KLG E+SE+F  PVILRL+TR+ H ++LV + E+++     + 
Sbjct: 134 HLPVLEPADSQEAYEMTKLGYELSERFQVPVILRLTTRICHVKALVTVGERQEHVGAGFK 193

Query: 184 YNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNKIEY-ANKKIGIITSGVAYNYAK 242
             P+++V  P+ A +R   + ER   L   A+ S +N IE  +++++G ITSG AY + K
Sbjct: 194 KEPARWVMTPSGAARRLPLMFEREAALKAEAEVSPLNVIEAGSDRRLGFITSGPAYMHVK 253

Query: 243 EAVSDASFLKFGMSYPLPEEKIKEFVQNCDKVYVFEELEPIFEQKIRSMGLNVIGKEIFP 302
           EA  +A  LK G S P P +K +E    CD+V V EE+EP+ E ++++ G+ + GK+I P
Sbjct: 254 EAFPEAPVLKLGFSCPAPIDKCRELAVLCDEVVVVEEVEPLLETELKAQGIALHGKDILP 313

Query: 303 IVGELSSEIIRNALLN------ESKIVIEKIEDLPQRPPVLCPGCHHRGPFYVLKKLK-L 355
            +GEL+  +++ A+         +   +  ++  P RPP +C  C H G +Y L +++ +
Sbjct: 314 RIGELAPPVLKAAIAKLRGEPVPAVTAVAPMQVFP-RPPTMCVACPHLGVYYTLSQVRNI 372

Query: 356 HVAGDIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGK-EFAKKSVAVIGDSTFWH 414
            +AGDIGCYTLG   P NA+DT I MGAS+G+A G +  RG+ +  K+ +AVIGDSTF H
Sbjct: 373 TIAGDIGCYTLGAGHPWNALDTCISMGASMGVALGLDKGRGESDKDKRILAVIGDSTFLH 432

Query: 415 SGVTGLIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTNQIDFEALGRSIGI 474
            G+ GL+DIVYN+G+ TV++LDN    MTG Q NP  G  + G    ++DF  L +++G+
Sbjct: 433 MGMQGLLDIVYNQGNVTVLLLDNRAVGMTGGQNNPGNGLDIHGNEAPRVDFVKLVQALGV 492

Query: 475 --NRICVVDAYDLKALEETIKEEVNAEEPSLIITKRPCVLIKGAKFDFKDYKIDPKLCTG 532
              R+  V+ Y+L  L + I+EEV   EPS+IIT +PCVL + A    K + +    CTG
Sbjct: 493 KPERVHKVNPYELPVLFKAIREEVKVAEPSVIITDQPCVLTE-AYHKLKPFTVMDDKCTG 551

Query: 533 CKLCLKAGCPAI--------------SFDGKVAKINDSLCVGCGLCKDLCKFSAIV 574
           C  C++ GCPAI                D    +I  + C GCGLC   C   AIV
Sbjct: 552 CGNCVEVGCPAIHVTRREKAIKPNGREVDLNFVRIETAACTGCGLCVQPCAPDAIV 607


Lambda     K      H
   0.317    0.136    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: 907
Number of extensions: 41
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: 578
Length of database: 621
Length adjustment: 37
Effective length of query: 541
Effective length of database: 584
Effective search space:   315944
Effective search space used:   315944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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