GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Thermithiobacillus tepidarius DSM 3134

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000423825.1:WP_028989221.1
          Length = 652

 Score =  809 bits (2089), Expect = 0.0
 Identities = 409/654 (62%), Positives = 488/654 (74%), Gaps = 10/654 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           +ES++ E RVF   E FA QA + S E Y ALC  AE D  GFW   AR+ L W KPFT+
Sbjct: 6   LESILTEARVFPVHEDFARQANLNS-EQYAALCRRAEEDPSGFWGDLARQELAWDKPFTQ 64

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VLD S APFY+WF DGELN + NCLDR+L +   +K A+++E +DG V   TY +LH +V
Sbjct: 65  VLDDSRAPFYRWFADGELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
            RFAN LK LGI  GDRV IYMPM  E  VAM ACARLGA HSVVFGGFSA++L++R+ D
Sbjct: 125 SRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIED 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A  LITAD   R G+ + LK  AD AL   G  +V  V+V RRTG +V   +GRD W 
Sbjct: 185 TQAKLLITADGGFRAGRVVHLKQHADQALMRDG-HSVDKVVVLRRTGQEVDMLDGRDLWW 243

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            ++       C A  V+AEHPLFVLYTSGSTGKPKG+ HS+GGYLLW+ +TM+W FDIKP
Sbjct: 244 HELMQDAEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKP 303

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
           +D++WCTADIGWVTGHTY  YGPLA GAT ++FEGVPTYP+AGRFW MI RH VS+FYTA
Sbjct: 304 EDVYWCTADIGWVTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTA 363

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTA+R+L+K  E      P +YDLSSLRLLGTVGEPINPEAWMWYY+ IG ERCP+VDT+
Sbjct: 364 PTAVRALMKLGEE----WPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTW 419

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGN-GGILVVKRPWPA 482
           WQTETGGH+I PLPG TPL PGSCT PLPGI   IVDE G  V     GG LVVKRPWP 
Sbjct: 420 WQTETGGHLIAPLPGVTPLKPGSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRPWPG 479

Query: 483 MIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGT 542
           M+RT+WG+  R+ ++Y+  +   + Y+AGD + RD D GY+ IMGRIDDVLNVSGHR+GT
Sbjct: 480 MLRTVWGNDARYLETYW-AKFQNRYYVAGDSAHRDAD-GYYWIMGRIDDVLNVSGHRLGT 537

Query: 543 MEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKE 602
           MEIESALVS+P VAEAAVVGRP ++ GEAI AFV+L++S    ++  ++   LR  V + 
Sbjct: 538 MEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSH-VQDDRDRLTEALRQHVSEA 596

Query: 603 IGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
           IGPIAKP DIRF DNLPKTRSGKIMRRLLR++A+GEEITQDTSTLEN   + QL
Sbjct: 597 IGPIAKPDDIRFTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETVRQL 650


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: 1406
Number of extensions: 78
Number of successful extensions: 9
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: 652
Length adjustment: 38
Effective length of query: 622
Effective length of database: 614
Effective search space:   381908
Effective search space used:   381908
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.

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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