GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Shewanella loihica PV-4

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 5210129 Shew_2573 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)

Query= metacyc::MONOMER-13597
         (509 letters)



>lcl|FitnessBrowser__PV4:5210129 Shew_2573 carbamoyl-phosphate
           synthase L chain, ATP-binding (RefSeq)
          Length = 677

 Score =  365 bits (938), Expect = e-105
 Identities = 193/456 (42%), Positives = 283/456 (62%), Gaps = 7/456 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+++L+ANRGEIA R++K  + MG+  +A+YS+ADK A H   ADE++Y+G +   +SYL
Sbjct: 2   FTKLLIANRGEIACRIIKTAQVMGIKTVALYSDADKDARHVAMADESFYLGGSAPSESYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
             E I++ A+++   AIHPGYGFLSENA+FA   E+AGI F+GPS++ +  +  K   K 
Sbjct: 62  KGELILEIAKRSGAQAIHPGYGFLSENADFARQCEQAGIAFVGPSADAIDAMGSKSAAKI 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           +   A VP  PG  G   S +  LK +++IG+P ++KAA GGGG G+  V+++ + ++  
Sbjct: 122 IMEQANVPLVPGYHGDDQSDEVLLKASKEIGFPQLIKAAYGGGGKGMRIVESESEALEAI 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              +R A  +FG   L IE+Y   PRH+E Q+  D  GN +   +R+C+IQRR+QK++EE
Sbjct: 182 NSARREAASSFGNDKLLIERYLRQPRHVEVQVFADTQGNCIYLSDRDCSIQRRHQKVVEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFE----TAFSDVSRDFYFLELNKRLQVE 299
           AP+P L    R +M E  +   K I+Y   GT E    T  ++ S  FYF+E+N RLQVE
Sbjct: 242 APAPGLSDSLRRAMGEAAVAAAKAIDYVGAGTVEFLLDTHATEESNSFYFMEMNTRLQVE 301

Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359
           HP TE++   DLVK Q+ +A+G  LP SQED+  R+ G + E RI AED  N F  +SG 
Sbjct: 302 HPVTEMVTGQDLVKWQLMVASGSELPLSQEDV--RIHGHSFEVRIYAEDPQNEFLPASGK 359

Query: 360 VTYYREP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418
           + + REP     VR+DSGI     +  +YD +++KLIV+ ESR  A+Q  + AL  Y+I 
Sbjct: 360 LNFLREPEQNRYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQIS 419

Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454
           G+K  IE    I +   F +  FST +I +  D  +
Sbjct: 420 GLKHNIEFLANIAEHKAFSQADFSTDFIERYGDTLI 455


Lambda     K      H
   0.317    0.135    0.385 

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: 757
Number of extensions: 39
Number of successful extensions: 4
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: 509
Length of database: 677
Length adjustment: 37
Effective length of query: 472
Effective length of database: 640
Effective search space:   302080
Effective search space used:   302080
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: 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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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