Alignments for a candidate for iorA in Coprobacter fastidiosus NSB1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Coprobacter fastidiosus NSB1

Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_009316885.1 NSB1T_RS15435 indolepyruvate ferredoxin oxidoreductase

Query= BRENDA::Q6LZB6
         (578 letters)



>NCBI__GCF_000473955.1:WP_009316885.1
          Length = 529

 Score =  358 bits (918), Expect = e-103
 Identities = 213/534 (39%), Positives = 314/534 (58%), Gaps = 41/534 (7%)

Query: 2   KKLMLGNEAVARGAYEAGVLVATAYPGTPSTEITEHISKYPE-----INSEWSVNEKVAL 56
           K L LG+EA+A+GA +AG+    AYPGTPSTEITE+I   PE     I++ W  NEK A+
Sbjct: 3   KHLFLGDEAIAQGALDAGLSGVYAYPGTPSTEITEYIQISPEAKNNTIHTRWCTNEKTAM 62

Query: 57  EVAIGSAIAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLIIVADDPSMHSSQNEQDT 116
           E A+G +  G R +V MKHVG+NVAAD  +    TG+N GL+++ ADDPSMHSSQNEQD+
Sbjct: 63  EAALGMSYIGKRALVCMKHVGMNVAADAFINAGMTGVNGGLIVVAADDPSMHSSQNEQDS 122

Query: 117 RYYGIFSKIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLV--ELEEK 174
           R+YG F+ +P+ EPS+ QE  D +  G  +SEKF  PV+LR++TR++HS++ V   L+ K
Sbjct: 123 RFYGNFAFVPMFEPSNQQEAYDMMAAGFGLSEKFKIPVLLRITTRLAHSRAGVTTTLKIK 182

Query: 175 EKIELKPYDYNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNK-IEYANKKIGIIT 233
           ++ E+  +  N  +++  PAN+++R   +    K+ +  +++S  N+ I+  NKK+GII 
Sbjct: 183 DQNEIS-FPDNTGQFILLPANSRRRFRTLLNEQKDFTEASENSSFNRYIDGPNKKMGIIA 241

Query: 234 SGVAYNYAKEAV---SDASFLKFGMSYPLPEEKIKEFVQNCDKVYVFEELEPIFEQKIRS 290
            G+AYNY  E      D   +K    YPLP + +++    CD++ V E+     E+KI+ 
Sbjct: 242 CGIAYNYLMENYPEGCDYPVVKLS-QYPLPLKMLQKLFDTCDEILVLEDGYAFVEEKIKG 300

Query: 291 MGLNVIGKEIFPIV----GELSSEIIRNALLNESKIVIEKIEDLPQRPPVLCPGCHHRGP 346
           +  + I K          GEL+ + +  AL  +S    E    +  RPP LC GC HR  
Sbjct: 301 IIPSKIIKGKLDGTLNRDGELNPDRVAKALGLKSGAEFEIPNIVAMRPPALCQGCGHRDM 360

Query: 347 FYVLKKL-----KLHVAGDIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGKEFAK 401
           +  L  +        +  DIGCYTLG   P  AI + + MGASI MA G   A G  F  
Sbjct: 361 YEALNNVAKTYKNARIFSDIGCYTLGALPPFRAIHSCVDMGASITMAKG--AADGGLF-- 416

Query: 402 KSVAVIGDSTFWHSGVTGLIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTN 461
            ++AVIGDSTF HSG+TGL+D V    + T++I DN  TAMTG Q++  TGK        
Sbjct: 417 PAIAVIGDSTFTHSGITGLLDCVNENANVTIVISDNETTAMTGGQDSAGTGK-------- 468

Query: 462 QIDFEALGRSIGIN----RICVVDAYDLKALEETIKEEVNAEEPSLIITKRPCV 511
               EA+ + IG+     R+ +    +++ +E TI+EE+  +  S++I +R C+
Sbjct: 469 ---IEAICKGIGVAPEHIRVLIPLKKNMEEMERTIREEIEYKGVSVLIPRRECI 519


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: 801
Number of extensions: 39
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: 578
Length of database: 529
Length adjustment: 36
Effective length of query: 542
Effective length of database: 493
Effective search space:   267206
Effective search space used:   267206
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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