GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 2629598430 Ga0074568_11495 acetyl-coenzyme A synthetase

Query= SwissProt::P31638
         (660 letters)



>IMG__TrieryIMS101_FD:2629598430
          Length = 655

 Score =  730 bits (1884), Expect = 0.0
 Identities = 361/657 (54%), Positives = 472/657 (71%), Gaps = 13/657 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IES++QE R+F PPE F   A I  +E Y+ L ++A+ + E FWA  A   L W + + K
Sbjct: 6   IESILQEKRLFQPPEKFVQTAQIKGIEQYKELYEKAKSNPEEFWAELAETELDWFQKWDK 65

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VL+    PF KWF +G++N SYNCLDR+L     +K A+++E + G    +TY +LH +V
Sbjct: 66  VLEWQ-PPFAKWFINGKINISYNCLDRHLTTWRRNKAALIWEGEPGDSRTITYAQLHREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
           C+ AN  K LG++KGDRV IYMPM  E  +AM ACAR+GA H+VVFGGFSA +L+ RLVD
Sbjct: 125 CQMANVFKQLGVKKGDRVGIYMPMIPEAAIAMLACARIGAPHTVVFGGFSADALKNRLVD 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A  ++TAD   R    +PLK   D AL + G  +V NV+V +RT  K+    GRD W 
Sbjct: 185 AEAKLVVTADGGWRKDAIVPLKEQVDKAL-MAGAPSVENVLVVKRTAQKIQMEPGRDHWW 243

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            D+       C AEP+ +E  LF+LYTSG+TG PKGV H+TGGY L+  +T KW FD++ 
Sbjct: 244 HDLQKSASGECPAEPMDSEDMLFILYTSGTTGTPKGVVHTTGGYNLYTHVTNKWAFDLQD 303

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
            D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P   N G  WD++ ++ V+IFYTA
Sbjct: 304 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCLWDVVEKYGVTIFYTA 363

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTAIR+L+K  E     HP   +L+SLRLLGTVGEPINPEAW+WY++ IG+ +CPIVDT+
Sbjct: 364 PTAIRALMKMGEQ----HPNSRNLTSLRLLGTVGEPINPEAWIWYHRVIGDSKCPIVDTW 419

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
           WQTETGG MITPLPGATP  PGS T P PGI+A IV+E G  V   NGG LVVK PWP M
Sbjct: 420 WQTETGGFMITPLPGATPTKPGSATFPFPGIIADIVNEEGESVDGNNGGYLVVKHPWPGM 479

Query: 484 IRTIWGDPERFRKSYFP---EELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           +RT++GDP+RFR++Y+     + G  +Y AGDG+ +D+D GYF +MGR+DDV+NV+GHR+
Sbjct: 480 MRTVYGDPDRFRRTYWEYLRPKNGEYIYFAGDGAHKDED-GYFWVMGRVDDVINVAGHRL 538

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTME+ESALVS+P VAEAAVVG+PD++ GE I AFV L+  R   E   K   EL+  V 
Sbjct: 539 GTMEVESALVSHPAVAEAAVVGKPDEVKGEDIVAFVSLEGGREPDENLEK---ELKQHVV 595

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
           KEIG IA+P +IRF D+LPKTRSGKIMRRLLRSLA G+EIT DTSTL++ ++L++L+
Sbjct: 596 KEIGAIARPGEIRFTDDLPKTRSGKIMRRLLRSLAAGQEITGDTSTLQDRSVLDKLR 652


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: 1419
Number of extensions: 73
Number of successful extensions: 7
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: 655
Length adjustment: 38
Effective length of query: 622
Effective length of database: 617
Effective search space:   383774
Effective search space used:   383774
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