GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Acidovorax sp. GW101-3H11

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Ac3H11_951 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= SwissProt::P31638
         (660 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 Acetyl-coenzyme A
           synthetase (EC 6.2.1.1)
          Length = 664

 Score = 1038 bits (2684), Expect = 0.0
 Identities = 495/659 (75%), Positives = 568/659 (86%), Gaps = 2/659 (0%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           SAIESV+ E+RVF P +     A +  M  Y ALC EA++D+EGFWAR ARE ++WTKPF
Sbjct: 6   SAIESVLVENRVFPPSDAVVKAARVSGMAGYDALCAEADKDFEGFWARLARENVNWTKPF 65

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
            + LD SNAPF+KWF+DGELNAS NCLDR++     +K AIVFEADDG+VTR+TY+EL  
Sbjct: 66  NRTLDTSNAPFFKWFDDGELNASANCLDRHIGTPTENKTAIVFEADDGTVTRITYKELLA 125

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +V +FAN LKA G+ KGDRV+IYMPM++EGV+AMQACAR+GATHSVVFGGFSAK++QER+
Sbjct: 126 RVSQFANALKAHGVTKGDRVLIYMPMTIEGVIAMQACARIGATHSVVFGGFSAKAVQERI 185

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241
           +D GAVA+ITA+ QMRGGK LPLKAI D+ALA+GGC+ +RNV VY+RT        GRD+
Sbjct: 186 IDAGAVAVITANYQMRGGKELPLKAIIDEALAMGGCDTIRNVFVYQRTATACNMVAGRDK 245

Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301
              ++ AGQ   C   PV AEHPLF+LYTSGSTGKPKGVQH+TGGYLLWA +TM WTFD+
Sbjct: 246 TFGEMLAGQSTECAPVPVGAEHPLFILYTSGSTGKPKGVQHATGGYLLWAKLTMDWTFDL 305

Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361
           + DD+FWCTADIGW+TGHTY+AYGPLAAGATQ++FEGVPT+PNAGRFW MI +HK +IFY
Sbjct: 306 RADDVFWCTADIGWITGHTYVAYGPLAAGATQIIFEGVPTFPNAGRFWQMIEKHKCTIFY 365

Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421
           TAPTAIRSLIKAAE D  +HP + DLSSLR+LG+VGEPINPEAWMWY+KN+G ERCPIVD
Sbjct: 366 TAPTAIRSLIKAAEGDAAVHPARSDLSSLRILGSVGEPINPEAWMWYHKNVGGERCPIVD 425

Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWP 481
           TFWQTETGGH+ITPLPGATPLVPGSCTLPLPGI AAIVDE G+DV NG GGILV+K+PWP
Sbjct: 426 TFWQTETGGHVITPLPGATPLVPGSCTLPLPGISAAIVDEMGNDVANGAGGILVIKKPWP 485

Query: 482 AMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMG 541
           +MIRTIW DPERF+K+YFPEEL G  YLAGDG++R  D GYF I GRIDDVLNVSGHRMG
Sbjct: 486 SMIRTIWNDPERFKKAYFPEELKG-YYLAGDGAVRSADRGYFRITGRIDDVLNVSGHRMG 544

Query: 542 TMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           TMEIESALVS   LVAEAAVVGRPDD+TGEAICAFVVLKRSRPTGEEA +IA ELRNWV 
Sbjct: 545 TMEIESALVSKTDLVAEAAVVGRPDDVTGEAICAFVVLKRSRPTGEEAKQIANELRNWVA 604

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS+AKGE ITQDTSTLENPAIL+QL +A
Sbjct: 605 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAILDQLAKA 663


Lambda     K      H
   0.319    0.136    0.422 

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: 1493
Number of extensions: 73
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: 660
Length of database: 664
Length adjustment: 38
Effective length of query: 622
Effective length of database: 626
Effective search space:   389372
Effective search space used:   389372
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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 paper from 2022 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