Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate H281DRAFT_05523 H281DRAFT_05523 propionyl-CoA synthetase (EC 6.2.1.17)
Query= reanno::Phaeo:GFF1175 (629 letters) >FitnessBrowser__Burk376:H281DRAFT_05523 Length = 648 Score = 642 bits (1656), Expect = 0.0 Identities = 320/639 (50%), Positives = 426/639 (66%), Gaps = 18/639 (2%) Query: 1 MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60 M+ E E W+ +P FW AA +++W + LT + + WF A N YN +DR Sbjct: 1 MNEGEFREDWRTDPMAFWARAASSVAWSRPWDEVLTHQPGQRFSWFDGAYTNASYNCLDR 60 Query: 61 HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120 HVE GRGEQ AI ++SP+T T + ++Y LR++VA AG L+ +GV GD V+IYMP+IP Sbjct: 61 HVEAGRGEQVAIAFESPVTGTAQTLTYASLRDQVAGFAGVLQLQGVRMGDVVVIYMPVIP 120 Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180 +A+ AMLACAR+GA H VVFGGFAA+ELA R+ D P+ I+ ASCG E R + YK +D Sbjct: 121 QAIIAMLACARIGATHCVVFGGFAASELAKRLRDTLPRVIVTASCGFEVKRRIPYKETVD 180 Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240 A+ L + +++QRE EL E RDV+W G +PV HP YIL+TS Sbjct: 181 EAV-LQSAWQGPVIVYQRELGRVELAE-RDVDWERAMCGTYGVSPIPVPAGHPLYILHTS 238 Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300 GTTG PKG+ R T G + AL W+M NIY PGDVFWAASD+GWVVGHSY+ YGPL++G Sbjct: 239 GTTGSPKGIQRDTGGYMTALLWSMNNIYRSLPGDVFWAASDIGWVVGHSYMTYGPLLNGC 298 Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDP---------KGEFVK 351 TT++FEGKP+GTPDA FWRVI++H+V FTAPTA RA+K+EDP GE Sbjct: 299 TTVLFEGKPVGTPDAAAFWRVIAKHRVNVLFTAPTALRAIKKEDPGGYQLREPVMGELHW 358 Query: 352 KYDLSCLKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANP----LGIEEL 407 +YDL L+ V+LAGER D TI WA++ L VPV+DHWWQTE GW +AA+ LG E Sbjct: 359 RYDLGSLRSVFLAGERCDTTTIEWAEDLLHVPVLDHWWQTEAGWPMAASTAKGALGGER- 417 Query: 408 PTKLGSPAVPMPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYL 467 + G+ +PG+ V +D+ G V G G + LPLPPG + T+WNA +R+++SY Sbjct: 418 --RRGAAGRALPGWDVRCVDDQGAEVDAGASGNVVCGLPLPPGAMTTIWNAHERYERSYF 475 Query: 468 TTFPGYYETGDAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIG 527 FPG+Y+TGDAG D DG++++M RTDDVINVAGHRLSTGA+EE+++ VAECAV+G Sbjct: 476 GRFPGWYDTGDAGYVDADGFVFVMGRTDDVINVAGHRLSTGAIEEIVSRLDAVAECAVVG 535 Query: 528 VSDSLKGQAPVGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSG 587 ++ LKGQ P+ FL L G + VK+VRE++G VA+ + A VV+RLPKTRSG Sbjct: 536 MAHPLKGQVPLVFLVLKDGSKDGADAAETAAVKVVREQLGAVASMQAAFVVERLPKTRSG 595 Query: 588 KILRGTMVNIADGTDWKMPATIDDPAILDEITTALQGLG 626 KILR +++ I DG +PATI+DP +L ++ ++ G Sbjct: 596 KILRRSLLQIVDGKAVAIPATIEDPGVLVDVERIVKARG 634 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: 1349 Number of extensions: 63 Number of successful extensions: 5 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: 648 Length adjustment: 38 Effective length of query: 591 Effective length of database: 610 Effective search space: 360510 Effective search space used: 360510 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