GapMind for catabolism of small carbon sources

 

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

Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate Ac3H11_209 Ferredoxin reductase

Query= reanno::WCS417:GFF4631
         (335 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_209
          Length = 328

 Score =  145 bits (367), Expect = 1e-39
 Identities = 105/316 (33%), Positives = 160/316 (50%), Gaps = 22/316 (6%)

Query: 25  LLDAALRNGIKIPLDCREGVCGTCQGRCESGDYSQDYVDEEALSSLDLQQRKMLSCQTRV 84
           LLDA     + +   C  G CG C+ R  SG+        E    LD     +L+CQT V
Sbjct: 20  LLDALRAAQVPMSYSCLSGRCGICRCRVLSGEVLDG--GREQQRPLDGVDGAVLACQTYV 77

Query: 85  KSDATFYFDFDSSLCNAPGPVQV------KGTVSAVEQVSASTAILQVQLDQALDFLPGQ 138
               T           APG   V      K TV A+E ++A    L +++ + + + PGQ
Sbjct: 78  TEPCTIEVP-------APGEAVVHRARVAKATVVAIEPLAADIRRLLLKVAKPIAYSPGQ 130

Query: 139 YARLSVPGTDSWRSYSFANLPGNHL-QFLVRLLPDGVMSNYLRERCQVGDELLMEAPLGA 197
           Y +L    T   R YS ANLPG  L +F ++L+P G +S Y+  + +VGD++ +  PLGA
Sbjct: 131 YMQLGFTPTHV-RPYSMANLPGEPLLEFHIQLMPQGRVSGYIAGQLKVGDKVKVSGPLGA 189

Query: 198 FYLRHV-TQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRGAEDLCEAARIRAY 256
            YLR   T P++ VAGGTGL+++L ++    A G   P+HLY+G+R   +L     +   
Sbjct: 190 AYLRQQHTGPMLCVAGGTGLASVLSVVRGAMAAGMRNPIHLYFGLRSPRELYGLTWLDHL 249

Query: 257 AAKIPNLRYTEVLSAPSEEWSGKRGYLTEHF--DLAELRDGSADMYLCGPPPMVESIQQW 314
            +  P L+   V+++ ++  + +RG +T+    D A L+   A  YLCG PPMVE+    
Sbjct: 250 RSVHPALQVHVVVASRADSATQRRGLVTQAIEQDHASLQGWQA--YLCGSPPMVETTTLL 307

Query: 315 LADQALDGVQLYYEKF 330
              + L+   L+ E F
Sbjct: 308 ALGKGLEAAHLHAEAF 323


Lambda     K      H
   0.320    0.136    0.412 

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: 318
Number of extensions: 23
Number of successful extensions: 6
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: 335
Length of database: 328
Length adjustment: 28
Effective length of query: 307
Effective length of database: 300
Effective search space:    92100
Effective search space used:    92100
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 (21.8 bits)
S2: 49 (23.5 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