GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Acidovorax sp. GW101-3H11

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 Ac3H11_2275 Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2275
          Length = 682

 Score =  380 bits (976), Expect = e-110
 Identities = 202/455 (44%), Positives = 287/455 (63%), Gaps = 13/455 (2%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+++L+ANRGEIA RV+   ++MG+  +AVYS+ADK A H K ADEA +IG AP+ +SYL
Sbjct: 2   FTKILIANRGEIACRVIATARKMGIATVAVYSDADKEARHVKLADEAVHIGAAPSRESYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
             + II A ++    A+HPGYGFLSEN  FA+  E  GI FIGP +  +  + DK+  K+
Sbjct: 62  LADKIIAACKQTGAQAVHPGYGFLSENEAFAKRCEDEGIAFIGPKAHSIAAMGDKIASKK 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           LAN A V T PG +  +   ++A+++A+ IGYP+M+KA++GGGG G+    N  +  + +
Sbjct: 122 LANEAKVNTIPGYNDAIAGPEQAVEIAKGIGYPVMIKASAGGGGKGLRVAFNDKEAFEGF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              +  A  +FG   +FIEK+   PRHIE Q++GD +GN +   EREC+IQRR+QK+IEE
Sbjct: 182 ASCQNEARNSFGDDRIFIEKFVQEPRHIEIQVLGDSHGNVIYLNERECSIQRRHQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           APSP +    R++M E  ++  K + Y + GT E       +DFYFLE+N RLQVEHP T
Sbjct: 242 APSPFISDATRKAMGEQAVQLAKAVKYQSAGTVEFVVGK-DQDFYFLEMNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E I  +DLV+L I++AAGE LP +Q D+ +   G AIE RINAED   NF  S+G +  +
Sbjct: 301 ECITGLDLVELMIRVAAGEKLPLTQADVKR--DGWAIECRINAEDPFRNFLPSTGRLVRF 358

Query: 364 REPTGP----------GVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALA 413
           + P             GVRVD+G+  G  +P YYDS+++KLIV+G  R  AI     AL 
Sbjct: 359 QPPEETMFQSDTTKKLGVRVDTGVYEGGEIPMYYDSMIAKLIVHGTDRNDAIAKMRAALN 418

Query: 414 DYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQ 448
            + I GI + I     ++  P F  G F+T +I++
Sbjct: 419 GFVIRGISSNIPFQAALLAHPKFVTGDFNTGFIAE 453


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: 747
Number of extensions: 26
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: 682
Length adjustment: 37
Effective length of query: 472
Effective length of database: 645
Effective search space:   304440
Effective search space used:   304440
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