Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 7024497 Shewana3_1675 AMP-dependent synthetase and ligase (RefSeq)
Query= metacyc::MONOMER-21334 (629 letters) >FitnessBrowser__ANA3:7024497 Length = 640 Score = 778 bits (2009), Expect = 0.0 Identities = 370/627 (59%), Positives = 468/627 (74%) Query: 2 AYQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRH 61 A Q ++++ ++ +AFW +AAK++DWV + LD+S AP Y WF+D ++NTC+NAVDRH Sbjct: 9 AGQQLHQTSIANKQAFWQQAAKALDWVTPSKQILDESEAPFYHWFSDGELNTCYNAVDRH 68 Query: 62 VEAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPE 121 V AGRGEQ AI Y SP+T T+ I+Y EL+ +VA LAG L++ GV KGDRV+IYMPM+PE Sbjct: 69 VLAGRGEQIAIHYVSPVTETEYSITYRELQAQVARLAGYLQSVGVAKGDRVVIYMPMVPE 128 Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDG 181 AMLACAR+GA+HSVVFGGFAANELA RI+DA+PK +++ASCG+EP VV YKPLLD Sbjct: 129 TAYAMLACARIGAIHSVVFGGFAANELATRINDAKPKLVMSASCGIEPSGVVPYKPLLDK 188 Query: 182 AIDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241 A++ A HK E C+I R Q A ++ GRD +W + A+CV V+ P Y+LYTSG Sbjct: 189 ALNEAVHKVEHCLILNRPQYEAQMQAGRDKDWQTALCTSDSADCVTVKATDPLYVLYTSG 248 Query: 242 TTGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301 TTG PKGV+R GH VAL W+M NIY++ GDVFWAASDVGWVVGHSYI YGPL+ G T Sbjct: 249 TTGQPKGVVRDNGGHAVALAWSMANIYDIAQGDVFWAASDVGWVVGHSYIVYGPLLVGAT 308 Query: 302 TIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKAL 361 T+++EGKPVGTPD G FWR I++++VKSFFTAPTAIRA+KREDP GE + DLS LK + Sbjct: 309 TLLYEGKPVGTPDPGAFWRTIAKYRVKSFFTAPTAIRAIKREDPDGEFILGVDLSCLKNV 368 Query: 362 YLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGY 421 +LAGER DPDT+ WA+ L PVIDHWWQTETGW +A N +G+ + K GSP + +PGY Sbjct: 369 FLAGERCDPDTLHWAEAKLHKPVIDHWWQTETGWPVAANLMGVAPIAVKAGSPGRPVPGY 428 Query: 422 DVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGM 481 +V ++DE G ++ G + +KLPLPPGTL LW R++ SYL +PGYY TGDAG Sbjct: 429 EVDVVDELGAKVAANVSGNVVIKLPLPPGTLTTLWQNNKRYQDSYLSMYPGYYLTGDAGY 488 Query: 482 IDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFL 541 +DEDGYLYIM+R DD+INVAGHRLSTG EEVL H DVAE AVIGV D LKGQ+PLG + Sbjct: 489 MDEDGYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHPDVAEAAVIGVDDKLKGQVPLGLV 548 Query: 542 CLNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGK 601 L G ++ K+++ LVR +IGPVA+F+L + +LPKTRSGKILRGTM IAD + Sbjct: 549 VLKKGVTITDEELHKQLIALVRQEIGPVASFRLVSAIQKLPKTRSGKILRGTMRKIADNQ 608 Query: 602 EYKMPATIDDPAILDEIKVALQSLGYA 628 +Y PATI+DP LD ++ L +GYA Sbjct: 609 QYTAPATIEDPQTLDLVRTTLTRMGYA 635 Lambda K H 0.319 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: 1303 Number of extensions: 53 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 ( 7.4 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 Apr 09 2024.
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