GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Nitratiruptor tergarcus DSM 16512

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_084275418.1 B8779_RS04840 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_900176045.1:WP_084275418.1
          Length = 650

 Score =  733 bits (1892), Expect = 0.0
 Identities = 367/654 (56%), Positives = 477/654 (72%), Gaps = 11/654 (1%)

Query: 8   MQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQ 67
           M++  VF+P      +A I SM+ Y  +  EAE DYEGFW + A+E ++W +P+TKVLD+
Sbjct: 1   MEKVPVFDPTPRIKERARINSMDQYWQMVKEAESDYEGFWDKLAKEKINWREPYTKVLDE 60

Query: 68  SNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFA 127
           S APFYKWF  G+LN +  C+DR+L+    +K AI++E + G    +TY EL+ +V RFA
Sbjct: 61  SEAPFYKWFVGGKLNVTEQCIDRHLET-KKNKAAIIWEGEPGDKRVITYLELYYEVNRFA 119

Query: 128 NGLKA-LGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGA 186
           N LK+  GI+KGDRVVIYMPM  E   AM ACAR+GA HSVVFGGFSA++L++R+ D  A
Sbjct: 120 NLLKSKFGIKKGDRVVIYMPMIPEAAFAMLACARIGAIHSVVFGGFSAEALRDRIQDAQA 179

Query: 187 VALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDV 246
             +ITAD   R GK   LK + D ALA   CE+V  V+V RR   ++ W + RD    ++
Sbjct: 180 KLVITADGAYRRGKPYMLKPVVDVALAKD-CESVEAVLVVRRNNEEIKWHDHRDYDYNEL 238

Query: 247 SAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDL 306
               P  CE E + +E PLF+LYTSGSTGKPKGVQHS  GY+LWA +TM+W FDIK  D 
Sbjct: 239 IKDMPARCEPEIMDSEDPLFLLYTSGSTGKPKGVQHSQAGYILWAQLTMEWVFDIKDTDT 298

Query: 307 FWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTA 366
           +WCTAD+GW+TGHTYI YGPLAAGAT +++EGVP YP+AGR+W MI  ++V+ FYTAPTA
Sbjct: 299 YWCTADVGWITGHTYIVYGPLAAGATTMMYEGVPVYPDAGRWWRMIEEYRVNQFYTAPTA 358

Query: 367 IRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQT 426
           IR L K   ADE   P +YDLSSL +LGTVGEPINP+AWMWY++ +G  +CPIVDT+WQT
Sbjct: 359 IRLLHKLG-ADE---PDKYDLSSLYILGTVGEPINPDAWMWYFEKVGRGQCPIVDTWWQT 414

Query: 427 ETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRT 486
           ETGGHMI+PLPGATP+ PGS T PLPGI A I+D  G+       G L + +PWP+MIRT
Sbjct: 415 ETGGHMISPLPGATPIKPGSATFPLPGIFAEIIDTDGNKKEPNEKGYLCITKPWPSMIRT 474

Query: 487 IWGDPERFRKSYFP--EELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTME 544
           IWGDP+RF KSYF   ++ G  +Y +GDG+I D++ GY  I GR+DDV+NVSGHR+GT E
Sbjct: 475 IWGDPDRFVKSYFGTCKKDGKPVYFSGDGAIYDEE-GYIWITGRMDDVINVSGHRLGTAE 533

Query: 545 IESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIG 604
           IE+A+  +P VAE AVVG+P ++ GE++ AFVVLK      +E +++  E+   + K+IG
Sbjct: 534 IEAAIGHHPRVAECAVVGKPHEVKGESVFAFVVLKDDEGVADE-MELIKEINEVITKDIG 592

Query: 605 PIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
           P+AK  +I F   LPKTRSGKIMRR+LRS+AKGEEI QDTSTLE+P+++E++ Q
Sbjct: 593 PLAKCDEIAFVPGLPKTRSGKIMRRILRSIAKGEEIKQDTSTLEDPSVVEKIIQ 646


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: 1347
Number of extensions: 81
Number of successful extensions: 8
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: 650
Length adjustment: 38
Effective length of query: 622
Effective length of database: 612
Effective search space:   380664
Effective search space used:   380664
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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