Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 3607411 Dshi_0825 AMP-dependent synthetase and ligase (RefSeq)
Query= reanno::Phaeo:GFF1175 (629 letters) >FitnessBrowser__Dino:3607411 Length = 630 Score = 1088 bits (2813), Expect = 0.0 Identities = 517/627 (82%), Positives = 560/627 (89%) Query: 1 MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60 M+YS+ Y WK +PE FWMEAA+AI W + P AL LYEWF DA VNTC+NAVDR Sbjct: 1 MTYSQTYAAWKNDPEGFWMEAAQAIDWVTPPGAALNSDNAPLYEWFTDAEVNTCFNAVDR 60 Query: 61 HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120 HV+ G G++ AII+DSP+THTK+EI+Y EL+ RV+ LAGALRAKG+EKGDRV+IYMPM+P Sbjct: 61 HVQAGNGDRVAIIHDSPVTHTKQEITYAELQERVSLLAGALRAKGIEKGDRVLIYMPMVP 120 Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180 +ALEAMLACARLGA+HSVVFGGFAANELAVRIDDATPKAIIAASCG+EPGR VHYKPLLD Sbjct: 121 QALEAMLACARLGAIHSVVFGGFAANELAVRIDDATPKAIIAASCGIEPGRVVHYKPLLD 180 Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240 GAIDLATHKPDFC+IFQREQEVA L GRD +WH QYGV+PAECVPV GNHPAYILYTS Sbjct: 181 GAIDLATHKPDFCLIFQREQEVAHLEPGRDFDWHEAQYGVDPAECVPVAGNHPAYILYTS 240 Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300 GTTGQPKGV+R TAG LVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICY PLIHGN Sbjct: 241 GTTGQPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYAPLIHGN 300 Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360 TTIVFEGKP+GTPDAGTFWRVISEHKVKSFFTAPTA RAVKREDP GEF+ KYDLS LK Sbjct: 301 TTIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTALRAVKREDPNGEFIGKYDLSHLKT 360 Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420 VYLAGERADPDTI W ++L VPVIDHWWQTETGW+IAANP+GIE LP K+GSP+V MPG Sbjct: 361 VYLAGERADPDTIQWTMDKLGVPVIDHWWQTETGWAIAANPMGIEHLPVKIGSPSVAMPG 420 Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480 Y V +LDEGGHPVAPG LGAIAVKLPL PGTLP LW AE+RF KSYLTTFPGYYETGDAG Sbjct: 421 YDVQVLDEGGHPVAPGTLGAIAVKLPLAPGTLPNLWQAEERFVKSYLTTFPGYYETGDAG 480 Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540 DEDGYLYIMARTDDVINVAGHRLSTGAMEEVLA HPDVAECAVIGVSD+LKGQ P+GF Sbjct: 481 YIDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGF 540 Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600 LCL+AG + PH+++ + VKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG Sbjct: 541 LCLSAGVNRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600 Query: 601 TDWKMPATIDDPAILDEITTALQGLGY 627 T WKMPATIDDPAILDEIT AL LGY Sbjct: 601 TPWKMPATIDDPAILDEITEALGKLGY 627 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: 1632 Number of extensions: 59 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 Sep 17 2021. 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