Alignments for a candidate for prpE in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Cupriavidus basilensis 4G11

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate RR42_RS13880 RR42_RS13880 AMP-dependent synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__Cup4G11:RR42_RS13880
          Length = 660

 Score = 1286 bits (3327), Expect = 0.0
 Identities = 619/660 (93%), Positives = 645/660 (97%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           MSAIESVMQEHR+FNPPE FA QAAIPSMEAYQALCDEAERDYEGFWARHARE LHWTKP
Sbjct: 1   MSAIESVMQEHRIFNPPESFAKQAAIPSMEAYQALCDEAERDYEGFWARHAREQLHWTKP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVLD+SNAPFYKWFEDGELNAS+NCLDRNL NGNA+KVAIVFEADDG+VTRVTYR+LH
Sbjct: 61  FTKVLDESNAPFYKWFEDGELNASFNCLDRNLDNGNAEKVAIVFEADDGTVTRVTYRQLH 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            KVC+FANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER
Sbjct: 121 AKVCQFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           LVDVGAVALITADEQMRGGKALPLKAIAD+ALALGGCEAV++VIVYRRTGGKV W EGRD
Sbjct: 181 LVDVGAVALITADEQMRGGKALPLKAIADEALALGGCEAVKSVIVYRRTGGKVNWAEGRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
           RWM+DV+AGQP TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKW+FD
Sbjct: 241 RWMDDVAAGQPQTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWSFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
           IKPDD+FWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF
Sbjct: 301 IKPDDMFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIKAAEADEKIHP+QYDLSSLRLLGTVGEPINPEAWMWYY+NIG ERCP+V
Sbjct: 361 YTAPTAIRSLIKAAEADEKIHPRQYDLSSLRLLGTVGEPINPEAWMWYYQNIGGERCPVV 420

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGI+AAIVDETG DVPNG+GGILVVKRPW
Sbjct: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIIAAIVDETGQDVPNGSGGILVVKRPW 480

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P+MIRTIWGDPERF+KSYFPEELGGKLYLAGDGSIRDK+TGYFTIMGRIDDVLNVSGHRM
Sbjct: 481 PSMIRTIWGDPERFKKSYFPEELGGKLYLAGDGSIRDKETGYFTIMGRIDDVLNVSGHRM 540

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALVSNP+VAEAAVVGRPDDMTGEAICAFVVLKRSRP  EEA +IA +LRNWVG
Sbjct: 541 GTMEIESALVSNPIVAEAAVVGRPDDMTGEAICAFVVLKRSRPNEEEAKQIAADLRNWVG 600

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660
           KEIGPIAKP+DIRFGDNLPKTRSGKIMRRLLRSLAK EEITQDTSTLENPAILEQLKQAQ
Sbjct: 601 KEIGPIAKPRDIRFGDNLPKTRSGKIMRRLLRSLAKNEEITQDTSTLENPAILEQLKQAQ 660


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: 1661
Number of extensions: 69
Number of successful extensions: 3
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: 660
Length adjustment: 38
Effective length of query: 622
Effective length of database: 622
Effective search space:   386884
Effective search space used:   386884
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources