Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate AZOBR_RS06340 AZOBR_RS06340 acyl-CoA synthetase
Query= reanno::Phaeo:GFF1175 (629 letters) >FitnessBrowser__azobra:AZOBR_RS06340 Length = 640 Score = 898 bits (2321), Expect = 0.0 Identities = 426/627 (67%), Positives = 500/627 (79%) Query: 3 YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHV 62 Y++++ ++P+ FW EAAE I+W K L D Y WF +NTCYNAVDRHV Sbjct: 9 YNQIHARSLSDPDGFWGEAAEDITWIKRWDKVLDDSNAPFYRWFTGGVLNTCYNAVDRHV 68 Query: 63 EQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEA 122 E GRG Q AIIYDSP+T T + I+Y E +++VA AGALRA+GVEKGDRVI+YMPMIP++ Sbjct: 69 EAGRGAQAAIIYDSPVTKTVQTITYAEFQDQVARFAGALRAQGVEKGDRVILYMPMIPQS 128 Query: 123 LEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGA 182 L AMLACARLGAVHSVVFGGFA +ELA RI+D+ PKAI++ASCG+EP R V YKP+LD A Sbjct: 129 LVAMLACARLGAVHSVVFGGFAPHELATRINDSRPKAIVSASCGIEPNRVVKYKPMLDAA 188 Query: 183 IDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGT 242 I+ A HKP ++FQR QE A L+EGRDV+W EPAECVPV P YILYTSGT Sbjct: 189 IEQAEHKPSSVIVFQRPQETATLVEGRDVDWAEAVAKAEPAECVPVAATDPLYILYTSGT 248 Query: 243 TGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTT 302 TGQPKGVIR G VAL WTMKNIYNV+PG+V+WAASDVGWVVGHSYI YGPL+HG TT Sbjct: 249 TGQPKGVIRDNGGHAVALKWTMKNIYNVEPGEVYWAASDVGWVVGHSYIVYGPLLHGCTT 308 Query: 303 IVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVY 362 +VFEGKP+GTPDAGTFWRVI +HK+ + FTAPTAFRA+KREDP E +KKYDLS + ++ Sbjct: 309 VVFEGKPVGTPDAGTFWRVIEQHKIGTLFTAPTAFRAIKREDPNAELLKKYDLSHFRALF 368 Query: 363 LAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYT 422 LAGER+DPDT+ WA++ L VPVIDHWWQTETGW+I+ NPLG+ P K GS PMPG+ Sbjct: 369 LAGERSDPDTLHWAEDNLNVPVIDHWWQTETGWAISGNPLGVHLFPIKYGSATRPMPGWD 428 Query: 423 VDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMK 482 V IL+ V G++GAI VKLPLPPGTLPTLWNA+DR++KSYL+ +PGYY+TGDAG Sbjct: 429 VQILNAENKEVPRGDIGAICVKLPLPPGTLPTLWNADDRYRKSYLSDYPGYYQTGDAGFI 488 Query: 483 DEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLC 542 D+DGY+YIMARTDD+INVAGHRLSTG MEEVLA H DVAECAVIGV+D LKGQ P+GFLC Sbjct: 489 DDDGYVYIMARTDDIINVAGHRLSTGGMEEVLASHKDVAECAVIGVADDLKGQVPLGFLC 548 Query: 543 LNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTD 602 L AG PHE++V +VV+LVRE+IGPVA FK A VV+RLPKTRSGKILRGTM IAD D Sbjct: 549 LKAGVTRPHEEIVKEVVQLVREQIGPVADFKRAVVVERLPKTRSGKILRGTMQKIADNQD 608 Query: 603 WKMPATIDDPAILDEITTALQGLGYAK 629 +K PATIDDP IL EI ALQ LGYAK Sbjct: 609 YKTPATIDDPGILPEIAEALQSLGYAK 635 Lambda K H 0.318 0.137 0.428 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: 1404 Number of extensions: 54 Number of successful extensions: 1 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: 629 Length of database: 640 Length adjustment: 38 Effective length of query: 591 Effective length of database: 602 Effective search space: 355782 Effective search space used: 355782 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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.
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:
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