GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Acidovorax sp. GW101-3H11

Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate Ac3H11_3427 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3427
          Length = 1243

 Score =  239 bits (610), Expect = 4e-67
 Identities = 153/394 (38%), Positives = 215/394 (54%), Gaps = 24/394 (6%)

Query: 24   NDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIYSTNITPDKTTGIGDYSY 83
            N A ++RG  LA AGDC  CH+  GG P  GG  M TP G IY+TN+TPD  TGIG +S+
Sbjct: 848  NAATIERGRLLAAAGDCAVCHTAPGGTPNTGGRAMETPFGKIYTTNLTPDAETGIGQWSF 907

Query: 84   DDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPW 143
              FQ+A+R G+++ G  LYPA PY S+A +SD+D+ ALYAY M   A  A+  K +++ +
Sbjct: 908  SAFQRAMREGISQGGKHLYPAFPYTSFAKMSDDDLTALYAYLMAQPAVRAEVPK-TELTF 966

Query: 144  PLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKA 203
            P S+R  +A W  +F  D   F+P     P   RG YLV+G+GHCGACHTPR+    E  
Sbjct: 967  PFSVRPLMAGWNALF-HDATPFKPDPTRPPEWNRGAYLVQGVGHCGACHTPRNALGAEL- 1024

Query: 204  LSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRN-DHTAAFGGM 262
                G   +LSG  A IDGW A  L G ++  +  W+ D L  +LR+G +  H +A G M
Sbjct: 1025 ----GGAAFLSG--AMIDGWEAPALTGLSKAPV-PWTADALYGYLRHGHSPQHGSASGPM 1077

Query: 263  TDVVEHSLQHLSDDDITAIARYLKSLGAKDASQTVFTQDDQ-----VAKALWKGDDSQTG 317
              VV   L HL DDDI A+A YL S  A +A+    +   Q     VA+A          
Sbjct: 1078 APVV-RELAHLPDDDIRAMASYLASFTAAEAATQPVSDPQQRAQTAVAQAAALAPQPGQA 1136

Query: 318  ASVYVDSCAACHKT-DGSRLSAL-LPGAAWQPGGAGEPDPTSLIHIVLTGGTLPGVQGAP 375
              ++  +CAACH   DG +L  + +P A      +  PD  +L+ +++ G   P  +   
Sbjct: 1137 QRLFDGACAACHHDGDGPKLLGVNVPLALNSNLHSDRPD--NLLQVIVHGIREPAARDIG 1194

Query: 376  TAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKA 409
                MP FG  L+D Q+ ++  ++R  +  G  A
Sbjct: 1195 ---FMPGFGHALSDAQITELAGYMRQRYAPGRPA 1225


Lambda     K      H
   0.317    0.133    0.409 

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: 1466
Number of extensions: 85
Number of successful extensions: 7
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: 441
Length of database: 1243
Length adjustment: 40
Effective length of query: 401
Effective length of database: 1203
Effective search space:   482403
Effective search space used:   482403
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 (21.6 bits)
S2: 55 (25.8 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:

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:

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:

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:

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