GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Trichormus variabilis ATCC 29413

Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= SwissProt::O06837
         (502 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  313 bits (802), Expect = 9e-90
 Identities = 181/487 (37%), Positives = 269/487 (55%), Gaps = 15/487 (3%)

Query: 22  QMLIGGQWVNAQSDKTLNVYNPAT-GDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMP 80
           Q  I GQW+NA ++ TLN +NPA   + +   P    +D + AV +A     S  WR++P
Sbjct: 8   QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGS--WRKVP 65

Query: 81  PSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLT 140
             AR   + R+ +LL  H +ELA+L +   GK +  ++  +V        Y AG   +L 
Sbjct: 66  APARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGRRLF 124

Query: 141 GSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPA 200
           G T    +P        A T R+P+GV A I PWNFP+ +  WK  PAL CGNTV+LKPA
Sbjct: 125 GQTTPSEMP-----NKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPA 179

Query: 201 EETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIG 260
           E+TP  A +L E+   AGLP G +N+V G GE AG ALV HP +  V+FTGS+  G  +G
Sbjct: 180 EDTPACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVG 239

Query: 261 SACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIY 320
             CGR+ K V LE+GGK+  +V+ D D + A +GA    F   GQ CTA SRL +H  I 
Sbjct: 240 ETCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIK 299

Query: 321 EDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGG---T 377
           E     L      + +G+G E    +GP+++ +  + V  ++    E+GA ++ GG   T
Sbjct: 300 EKFTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVT 359

Query: 378 EAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGAS 437
           E    QG+F +PTI  N     +R+  +E+FGPV+     S   E +   N + YGL +S
Sbjct: 360 EGQLKQGYFFQPTILDN-VTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSS 418

Query: 438 IWTNDLSAALRINDELEAGTVWVNTHNM-VDPNLPFGGFKDSGVG-REHGAAAIEHYTTT 495
           ++T D++ A     ++E G  ++N   +  + +LPFGG K +G G RE G  A++ +T  
Sbjct: 419 VYTRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEW 478

Query: 496 RSLVIAY 502
           +S+ + +
Sbjct: 479 KSVYVDF 485


Lambda     K      H
   0.317    0.134    0.395 

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: 594
Number of extensions: 28
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: 502
Length of database: 498
Length adjustment: 34
Effective length of query: 468
Effective length of database: 464
Effective search space:   217152
Effective search space used:   217152
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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