GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Shewanella sp. ANA-3

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 7024491 Shewana3_1669 3-methylcrotonoyl-CoA carboxylase, alpha subunit (RefSeq)

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



>FitnessBrowser__ANA3:7024491
          Length = 674

 Score =  372 bits (956), Expect = e-107
 Identities = 204/492 (41%), Positives = 290/492 (58%), Gaps = 6/492 (1%)

Query: 5   SRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLN 64
           +++L+ANRGEIA R++K  + MG+  +A+YS+ADK A H   ADE++Y+G +   DSYL 
Sbjct: 3   TKLLIANRGEIACRIIKTAQAMGVRTVALYSDADKNARHVAMADESFYLGGSAPADSYLK 62

Query: 65  IEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRL 124
            + II+ A+KA   AIHPGYGFLSENA+FA   E AGI F+GP S+ +  +  K   K +
Sbjct: 63  GDLIIEIAKKAQAQAIHPGYGFLSENADFARKCEAAGIVFVGPGSDAIDAMGSKSAAKAI 122

Query: 125 ANMAGVPTAPGSDGPVTSIDEALKL-AEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
              A VP  PG  G     D  LK  A KIG+P+++KAA GGGG G+  V+++ ++MD  
Sbjct: 123 MTAAQVPLVPGYHGD-DQTDATLKAEALKIGFPMLIKAAYGGGGKGMRIVEHEGEIMDAI 181

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

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           AP+P L  E R  M E  +   K I+Y   GT E    D    FYF+E+N RLQVEHP T
Sbjct: 242 APAPGLSDELRTQMGEAAVAAAKAIDYVGAGTVEFLL-DTDNSFYFMEMNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E++   DLVK Q+ +A+G+ LP  Q+++  R+ G A E RI AED  N F  +SG + + 
Sbjct: 301 EMVTGQDLVKWQLMVASGQPLPLKQDEV--RIHGHAFEVRIYAEDPQNEFLPASGKLNFL 358

Query: 364 REP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
           REP     VR+DSGI     +  +YD +++KLIV+ ESR  A+Q  + AL  Y+I G+K 
Sbjct: 359 REPEQSKYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISGLKH 418

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSST 482
            IE    I + P F +  FST +I++  D  +     + +   A AA  Q       +  
Sbjct: 419 NIEFLANIAEHPAFAKADFSTDFINRYGDALISSASSETDTALAFAALYQVLARKEAAKA 478

Query: 483 DNKGKAQSKSGW 494
                A   S W
Sbjct: 479 QAINSADPYSPW 490


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: 776
Number of extensions: 34
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: 674
Length adjustment: 37
Effective length of query: 472
Effective length of database: 637
Effective search space:   300664
Effective search space used:   300664
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