Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011840264.1 RSPH17029_RS01250 propionyl-CoA synthetase
Query= reanno::Phaeo:GFF1175 (629 letters) >NCBI__GCF_000015985.1:WP_011840264.1 Length = 630 Score = 1023 bits (2646), Expect = 0.0 Identities = 488/629 (77%), Positives = 551/629 (87%) Query: 1 MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60 M+Y+ +Y+ +P FWM+AAE I W S P+KAL D+ + YEWFAD +VN C+NAVDR Sbjct: 1 MAYASLYKWSLEDPNGFWMKAAEQIDWVSPPSKALFDEKEPFYEWFADGQVNACWNAVDR 60 Query: 61 HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120 HVE GRG+Q AI+++SPITH+ + I+Y EL+ RVA+LAGALRAKGVEKGDRVIIYMPMIP Sbjct: 61 HVEAGRGKQIAIVHESPITHSSKGITYAELQARVASLAGALRAKGVEKGDRVIIYMPMIP 120 Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180 EALEAMLACARLGA+HSVVFGGFAA+ELAVRIDD TPKAIIAASCGLEP R VHYKPLLD Sbjct: 121 EALEAMLACARLGAIHSVVFGGFAAHELAVRIDDCTPKAIIAASCGLEPSRVVHYKPLLD 180 Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240 AI+ ATHKPDFCVIFQREQEVA+LIEGRDV WH FQYGVEPAECVPVEGNHPAYILYTS Sbjct: 181 QAIEEATHKPDFCVIFQREQEVAKLIEGRDVAWHTFQYGVEPAECVPVEGNHPAYILYTS 240 Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300 GTTGQPKGV+R T G LVALNWTMK IY++D GDVFWAASDVGWVVGHSYICYGPLI G Sbjct: 241 GTTGQPKGVVRATGGHLVALNWTMKAIYDIDAGDVFWAASDVGWVVGHSYICYGPLIAGA 300 Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360 TTIV+EGKP+GTPDAG FWRV+ HKVK+FFTAPTA RA+KREDP+G ++ Y+L LK Sbjct: 301 TTIVYEGKPVGTPDAGAFWRVMQNHKVKTFFTAPTALRAIKREDPQGALIQDYNLRNLKA 360 Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420 ++LAGERADPDTI WAQ+ + VPVIDHWWQTE+GW++AANPLGIE LP K+GSP++PMPG Sbjct: 361 LFLAGERADPDTIVWAQKNVGVPVIDHWWQTESGWAMAANPLGIEALPVKIGSPSLPMPG 420 Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480 Y V +LDEGGH + G+LGAIA+KLPLPPGTLPTLWNA+DRF KSYLT FPGYYETGDAG Sbjct: 421 YDVRVLDEGGHQLEAGQLGAIAIKLPLPPGTLPTLWNAQDRFVKSYLTHFPGYYETGDAG 480 Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540 DEDGY+YIMARTDDVINVAGHRLSTGAMEEVLA H DVAECAVIGV+D+LKGQ+P+GF Sbjct: 481 YIDEDGYIYIMARTDDVINVAGHRLSTGAMEEVLASHEDVAECAVIGVTDALKGQSPLGF 540 Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600 LCLN G + EDVV + VKLVREKIGPVA FK ACVVDRLPKTRSGKILRGTMV IADG Sbjct: 541 LCLNKGSNRAAEDVVKECVKLVREKIGPVADFKRACVVDRLPKTRSGKILRGTMVKIADG 600 Query: 601 TDWKMPATIDDPAILDEITTALQGLGYAK 629 ++KMPATIDDPAILDEI AL+ +GY + Sbjct: 601 QEFKMPATIDDPAILDEIRVALEAVGYPR 629 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: 1524 Number of extensions: 56 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: 630 Length adjustment: 38 Effective length of query: 591 Effective length of database: 592 Effective search space: 349872 Effective search space used: 349872 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 10 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