GapMind for Amino acid biosynthesis

 

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 Aug 03 2021. The underlying query database was built on Aug 03 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