GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Alicycliphilus denitrificans K601

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013518028.1 ALIDE2_RS18585 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000204645.1:WP_013518028.1
          Length = 665

 Score = 1069 bits (2764), Expect = 0.0
 Identities = 508/660 (76%), Positives = 581/660 (88%), Gaps = 5/660 (0%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           SAIESV+ E+RVF PPEG    A I  M  Y+ALC EA++D+EGFWAR ARE L WT+PF
Sbjct: 6   SAIESVLIENRVFPPPEGLVKTARISGMAGYEALCAEADKDFEGFWARLARENLQWTRPF 65

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
           TK LD+SNAPFY+WF DGELNAS NCLDR++      K AI+FEADDG+VT+VTY+EL  
Sbjct: 66  TKTLDESNAPFYQWFADGELNASANCLDRHMGTPVESKTAIIFEADDGAVTKVTYKELLA 125

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +V +FAN LKA G++KGDRV+IYMPM++EGVVAMQACAR+GATHSVVFGGFSAK++QER+
Sbjct: 126 RVAQFANALKAQGVKKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGGFSAKAVQERI 185

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWT--EGR 239
           +D GAVA+ITA+ Q+RGGK LPLKAI D+ +A+GGCE++++V+VY RT    AW   +GR
Sbjct: 186 IDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCESIKSVLVYERT--PTAWNRVDGR 243

Query: 240 DRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTF 299
           D+   +  AGQ   C    V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA +TM WTF
Sbjct: 244 DKSFAEALAGQSTECVPVAVEAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAKLTMDWTF 303

Query: 300 DIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSI 359
           D++PDD+FWCTADIGWVTGHTYIAYGPLAAG TQV+FEG+PTYPNAGRFW MI RHKVSI
Sbjct: 304 DLRPDDVFWCTADIGWVTGHTYIAYGPLAAGGTQVMFEGIPTYPNAGRFWQMIERHKVSI 363

Query: 360 FYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPI 419
           FYTAPTAIRSLIKAA++DEK+HPK +DLSSLR+LG+VGEPINPEAWMWYYKN+G ERCPI
Sbjct: 364 FYTAPTAIRSLIKAADSDEKVHPKNWDLSSLRILGSVGEPINPEAWMWYYKNVGGERCPI 423

Query: 420 VDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRP 479
           VDT+WQTE GGH+ITPLPGATPLVPGSCTLPLPGI AAIVDETG DVPNG+GG+LV+KRP
Sbjct: 424 VDTWWQTENGGHLITPLPGATPLVPGSCTLPLPGIAAAIVDETGKDVPNGSGGMLVIKRP 483

Query: 480 WPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539
           WP+MIRTIW DPERF+KSYFPEE+GGK+YLAGDG++RD  T YF + GRIDDVLNVSGHR
Sbjct: 484 WPSMIRTIWNDPERFKKSYFPEEMGGKIYLAGDGAVRDAKTAYFRVTGRIDDVLNVSGHR 543

Query: 540 MGTMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNW 598
           MGTMEIESALV+ + LVAEAAVVGRPDD+TGEAICAFVVLKR+RPTGEEA +IA ELRNW
Sbjct: 544 MGTMEIESALVAKSDLVAEAAVVGRPDDLTGEAICAFVVLKRARPTGEEAKQIAAELRNW 603

Query: 599 VGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
           V KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGE ITQDTSTLENPAIL+QL Q
Sbjct: 604 VAKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPAILDQLAQ 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: 1552
Number of extensions: 69
Number of successful extensions: 2
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: 665
Length adjustment: 38
Effective length of query: 622
Effective length of database: 627
Effective search space:   389994
Effective search space used:   389994
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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