GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Magnetospirillum magneticum AMB-1

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 WP_043746657.1 AMB_RS13620 acetyl-CoA carboxylase biotin carboxylase subunit

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



>NCBI__GCF_000009985.1:WP_043746657.1
          Length = 447

 Score =  398 bits (1023), Expect = e-115
 Identities = 206/445 (46%), Positives = 294/445 (66%), Gaps = 5/445 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F +VL+ANRGEIA R+ +A +EMG+  +AV+S AD  A+H + ADEA  IG   A DSYL
Sbjct: 2   FEKVLIANRGEIALRIHRACREMGIRTVAVHSTADNDAMHVRLADEAVCIGPPSARDSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           N   I+ AA     DAIHPGYGFLSENA+FA+ VE+ G  FIGP+ + +R + DK+  K+
Sbjct: 62  NKAAILSAASITGADAIHPGYGFLSENADFAQMVEEHGFVFIGPTPDHIRMMGDKITAKQ 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
               AG+P  PGSDG V + + AL++A  IGYP+++KA +GGGG G+    N ++L++ W
Sbjct: 122 AVKDAGIPVVPGSDGSVDTEETALEVAASIGYPVLIKATAGGGGKGMKVARNAEELVESW 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           +  +  A  AFG AD+++EKY   PRHIE Q++ D YG  V   ER+C++QR++QK++EE
Sbjct: 182 KLARNEAKAAFGNADVYMEKYLGKPRHIEMQILADNYGAVVHLGERDCSLQRKHQKVLEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           APSPAL  ++R  + +        + Y   GT E  +   + +FYF+E+N RLQVEHP T
Sbjct: 242 APSPALNADQRARIGKIACDAIAKLGYRNAGTIEFLYE--NGEFYFIEMNTRLQVEHPIT 299

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E I  IDLV+ QI++AAG  L ++Q D+  R  G A+E R+NAED +  FT   G +  Y
Sbjct: 300 EAITGIDLVREQIRIAAGAPLGYTQADV--RFAGHALECRVNAEDPV-TFTPCPGRIEGY 356

Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423
             P G GVRVDSG+ +G  +PP+YDS+++KLIV+G +R  A+    RAL +Y I G+KTT
Sbjct: 357 HAPGGLGVRVDSGLYAGYRIPPHYDSMIAKLIVFGNTRNEALMRLKRALGEYVIEGVKTT 416

Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448
           + L+  ++QD DF  G +   ++ +
Sbjct: 417 LPLHNRLVQDADFVNGDYDIHWLEK 441


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: 575
Number of extensions: 23
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: 447
Length adjustment: 33
Effective length of query: 476
Effective length of database: 414
Effective search space:   197064
Effective search space used:   197064
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:

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