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 5210426 Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)

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



>FitnessBrowser__PV4:5210426
          Length = 1094

 Score =  296 bits (757), Expect = 3e-84
 Identities = 173/448 (38%), Positives = 259/448 (57%), Gaps = 7/448 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+R+L+ANRGEIA R+ +   +MG+ ++A+Y+E D  ++HTK AD+A  + K   + +YL
Sbjct: 5   FNRILIANRGEIAIRIAQTCADMGIDSLAIYAEDDSQSLHTKKADQAVAL-KGRGVKAYL 63

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           +IE +I  A+    DA+HPGYGFLSEN+ F++   + GI FIG S+E++  + +K   + 
Sbjct: 64  DIEQLIAVAKAHGCDAVHPGYGFLSENSSFSKRCHEEGICFIGSSAELLDLLGNKATARE 123

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIG--YPIMVKAASGGGGVGITRVDNQDQLMD 181
            A  +  P   G + P  S++E       +G    +M+KA +GGGG G+  V   + L +
Sbjct: 124 TALRSDTPLTGGINKPC-SLEEVQAFFTSLGDGAAVMIKALAGGGGRGMRPVSRYEDLAE 182

Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241
            + + +  A  AFG  +L++E+   + RHIE Q++GD  G  V AWERECT+QRRNQKL+
Sbjct: 183 AYRQCREEAIIAFGSGELYVEQLVQHARHIEVQILGDGTGAAVHAWERECTLQRRNQKLL 242

Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAF-SDVSRDFYFLELNKRLQVEH 300
           E APSP+L    R  + E  ++    + Y  LGTFE    +D    FYF+E+N R+QVEH
Sbjct: 243 EIAPSPSLDDATRMPIIESALQLASDVKYQGLGTFEFLLDADDHSKFYFMEINPRIQVEH 302

Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDAL--NNFTGSSG 358
             TE I  ++LVKLQI L AG+ L           RG AI+ RIN E  L   +   +SG
Sbjct: 303 TITEEITGLNLVKLQILLGAGKTLAELSLTEAPIKRGCAIQARINLEQMLPDGSTKPASG 362

Query: 359 FVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418
            +  Y+ P G  VRVD  + +G  V P YDSL +K+I  GE    A+     +L    I 
Sbjct: 363 VIKAYQVPNGHNVRVDDYLYAGYKVSPSYDSLGAKIIAKGEDFSAALNKVYLSLKALNID 422

Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYI 446
           G+++   L   ++Q  + Q  + ST ++
Sbjct: 423 GVQSNKALLMNLLQREEVQHNRLSTRFV 450


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: 1151
Number of extensions: 56
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 509
Length of database: 1094
Length adjustment: 40
Effective length of query: 469
Effective length of database: 1054
Effective search space:   494326
Effective search space used:   494326
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: 55 (25.8 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