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 5210939 Shew_3365 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)

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



>lcl|FitnessBrowser__PV4:5210939 Shew_3365 acetyl-CoA carboxylase,
           biotin carboxylase (RefSeq)
          Length = 450

 Score =  363 bits (932), Expect = e-105
 Identities = 192/449 (42%), Positives = 291/449 (64%), Gaps = 6/449 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           M  F +VLVANRGEIA R+++A +++G+  +A+YS ADK + H + AD+   IG APA +
Sbjct: 1   MRRFDKVLVANRGEIALRIIRACRQLGIKTVALYSSADKDSGHLRLADQQICIGPAPAKE 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYLNI  I+ AA+ A VDAIHPGYGFL+ENA+FA+ V  +G  FIGP ++ +R + DK+ 
Sbjct: 61  SYLNIAAILGAADLARVDAIHPGYGFLAENADFAQQVTDSGFHFIGPKADTIRLMGDKVS 120

Query: 121 GKRLANMAGVPTAPGSDGPVTSID-EALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179
                  AGVPT PGSDG +   + ++L++A +IGYP+++KA +GGGG G+  V+++ QL
Sbjct: 121 AIAAMKAAGVPTVPGSDGLLGDNEAQSLEIAAQIGYPLIIKATAGGGGKGMRVVEDEAQL 180

Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239
           +      ++ A  AFG   +++EKY   PRHIE Q++ D  G+ +   ER+C++QR  QK
Sbjct: 181 LGAIALTRQEAEAAFGNGGVYLEKYLTRPRHIEVQVLCDHQGHCISLGERDCSLQRAQQK 240

Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299
           +IE AP+P L  E+R+ + E  I+  + I Y   GT E  + D   +FYF+E+N R+QVE
Sbjct: 241 VIESAPAPGLTPEQRQQISESCIRACQAIGYRGAGTLEFLYQD--GEFYFMEMNTRIQVE 298

Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359
           H  +E++  +DL+ LQ+++A GE  P + ++   + +G AIE RINAED   +F  S G 
Sbjct: 299 HTISEMVTGVDLLVLQLRVAQGE--PLALQESLIQPKGHAIECRINAEDPA-SFAPSPGR 355

Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419
           +     P G GVR +S +  G++VPP YD++++KLI +G+ R  AI     AL +  I G
Sbjct: 356 IDRLVVPGGLGVRWESHLSPGAHVPPQYDAMIAKLIAWGDDRAQAIARMRTALDELTITG 415

Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQ 448
           IKT + L + ++ DP  Q+G+ S  Y+ +
Sbjct: 416 IKTNVPLLRALLADPQVQQGETSIHYLEE 444


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: 498
Number of extensions: 24
Number of successful extensions: 5
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: 450
Length adjustment: 34
Effective length of query: 475
Effective length of database: 416
Effective search space:   197600
Effective search space used:   197600
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: 51 (24.3 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