GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Marinobacter adhaerens HP15

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 GFF3280 HP15_3222 acetyl-CoA carboxylase biotin carboxylase subunit

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



>lcl|FitnessBrowser__Marino:GFF3280 HP15_3222 acetyl-CoA carboxylase
           biotin carboxylase subunit
          Length = 448

 Score =  381 bits (979), Expect = e-110
 Identities = 202/449 (44%), Positives = 295/449 (65%), Gaps = 6/449 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           M    +VL+ANRGEIA R+L+A KE+G+  +AV+S+ D+  +H + ADE+  IG   A D
Sbjct: 1   MAMLEKVLIANRGEIALRILRACKELGIKTVAVHSQVDRDLMHVRLADESVCIGPNSATD 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYLNI  II AAE      IHPGYGFL+ENA+FAE VEK+G  FIGP +E +R + +K+ 
Sbjct: 61  SYLNIPTIISAAEVTDSVGIHPGYGFLAENADFAEQVEKSGFRFIGPKAETIRLMGNKVS 120

Query: 121 GKRLANMAGVPTAPGSDGPVTSIDE-ALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179
                  AGVPT PGSDGP+   +E  L++A++IGYP+M+KAASGGGG G+  V ++  L
Sbjct: 121 AINAMIKAGVPTVPGSDGPLDDDEERTLRIAKEIGYPVMIKAASGGGGRGMQVVHSEAAL 180

Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239
           +   +  +  A  AFG   +++EK+   PRH+E Q++ D +GN +   +R+C++QRRNQK
Sbjct: 181 LKGVQITQSEAKNAFGDPTVYLEKFLEAPRHVEVQVLADMHGNCIHLGDRDCSMQRRNQK 240

Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299
           +IEEAP+P +  E RE   +      K I Y   GTFE  + D   +FYF+E+N R+QVE
Sbjct: 241 VIEEAPAPNINPESRERTLKACTDACKEIGYVGAGTFEFLYQD--GEFYFIEMNTRVQVE 298

Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359
           HP +E++  +D+V+ Q+++A+G  L ++Q+D+  R+ G A+E RINAED    F  S G 
Sbjct: 299 HPVSEMVTGVDIVREQLRIASGLPLQYTQDDI--RISGHAMECRINAEDP-KTFIPSPGK 355

Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419
           V ++  P G GVRVDS + SG  VPPYYDSLV+KLI +G+ R+ A +    AL +  + G
Sbjct: 356 VKHFHAPGGNGVRVDSHLYSGYTVPPYYDSLVAKLITWGDDRDIARRRMKNALDELVVEG 415

Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQ 448
           IKT   L++ +++D  F++  F+  Y+ +
Sbjct: 416 IKTNQPLHRKLVRDGGFKQVDFTIHYLEK 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: 534
Number of extensions: 20
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: 448
Length adjustment: 34
Effective length of query: 475
Effective length of database: 414
Effective search space:   196650
Effective search space used:   196650
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 preprint 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