Alignments for a candidate for pccA1 in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA1 in Shewanella amazonensis SB2B

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 6939098 Sama_3196 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)

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



>FitnessBrowser__SB2B:6939098
          Length = 454

 Score =  334 bits (856), Expect = 5e-96
 Identities = 188/435 (43%), Positives = 269/435 (61%), Gaps = 10/435 (2%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F RVLVANRGEIA R+++A  ++G+  +A+YS ADK A+HT  A     IG A A DSYL
Sbjct: 7   FKRVLVANRGEIAVRIIRACHQLGLETVAIYSSADKGALHTLLATHCLCIGPAAAKDSYL 66

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           NI  I++AA+    DAIHPGYGFL+E A FA AV +AG+ F+GP ++ +  + DK+   +
Sbjct: 67  NINAILEAAKLTAADAIHPGYGFLAERAGFARAVTEAGLVFLGPDADTIATMGDKVSAIK 126

Query: 124 LANMAGVPTAPGSDGPVTSIDEALK-LAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182
                G+PT PGSDG +     A++ LA  IGYP+++KA++GGGG G+ RVD+ D+L   
Sbjct: 127 SIKAVGIPTLPGSDGALNDDMNAVEALATDIGYPVLIKASAGGGGRGMRRVDSADELASA 186

Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242
               +  A  AFG   +++EK+  +PRHIEFQ++ D      +  ER+C+ QRR+QKLIE
Sbjct: 187 IALTRSEALAAFGDNTVYLEKFLTHPRHIEFQMLADGEAALCLG-ERDCSAQRRHQKLIE 245

Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302
           EAP+  +  E+   M +      + + Y  +GTFE  + D +  F+F+E+N R+QVEH  
Sbjct: 246 EAPALGIAREKIREMADICEAACRRLGYRGVGTFEFLYQDGA--FFFIEMNTRIQVEHTV 303

Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362
           TE++  +DL+  Q+K+A G  LP        +V+G AIE RINAE A  +   S G +T 
Sbjct: 304 TEMVTGLDLIAWQLKVALGHPLP-----PRPQVQGHAIECRINAE-APQSQLPSPGVITQ 357

Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
            R P GPGVR DS +  G+ VP +YDSL+ KLI +G +RE A     +AL + +I GI  
Sbjct: 358 LRVPGGPGVRWDSYLFPGAMVPAFYDSLIGKLICHGVTREEATARLRQALTELEIQGIAI 417

Query: 423 TIELYKWIMQDPDFQ 437
              L+  ++    FQ
Sbjct: 418 NKSLHLQLIACDAFQ 432


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: 539
Number of extensions: 26
Number of successful extensions: 6
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: 454
Length adjustment: 34
Effective length of query: 475
Effective length of database: 420
Effective search space:   199500
Effective search space used:   199500
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources