GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF3280
          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:

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