GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5210129
          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:

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