Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011427294.1 RHE_RS21035 propionyl-CoA synthetase
Query= reanno::Phaeo:GFF1175 (629 letters) >NCBI__GCF_000092045.1:WP_011427294.1 Length = 636 Score = 810 bits (2093), Expect = 0.0 Identities = 388/631 (61%), Positives = 475/631 (75%), Gaps = 10/631 (1%) Query: 3 YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLY-EWFADARVNTCYNAVDRH 61 Y + Y WK++PE FW EAA I W P + + +G+Y WF+ A NTC+N +DRH Sbjct: 5 YHQTYAAWKSDPEAFWREAAADIDWFKPPERVYSPD-EGIYGRWFSGAETNTCHNCLDRH 63 Query: 62 VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121 V GRG +TAII+DS +T KR SY E+ V +A L A G+ +GDRVI+YMPM+P+ Sbjct: 64 VRAGRGGETAIIFDSAMTGEKRRFSYDEVLGEVKAIAETLLALGIARGDRVILYMPMLPQ 123 Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181 A+ +MLACAR+GAVHSVVFGGFAA+ELA RIDD+ + +I ASCGLEPGR V YKPL+D Sbjct: 124 AVFSMLACARIGAVHSVVFGGFAASELAARIDDSGARLVITASCGLEPGRVVAYKPLVDQ 183 Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEP-----AECVPVEGNHPAYI 236 AI++A KP+ C++ QR Q AEL+ GRD + F+ V P CV V P YI Sbjct: 184 AIEIARMKPERCLVLQRPQLRAELVGGRDED---FEAAVAPHRGAEVACVSVRATDPLYI 240 Query: 237 LYTSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPL 296 LYTSGTTGQPKGV+R G +VALNW+M+NIY + PG+VFW ASD+GWVVGHSYI Y PL Sbjct: 241 LYTSGTTGQPKGVVRDNGGHMVALNWSMRNIYGLKPGEVFWTASDIGWVVGHSYIVYAPL 300 Query: 297 IHGNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLS 356 I G TT++FEGKP+GTPDAG FWR+++EH V+ FTAPTAFRA++RED GE + +Y++ Sbjct: 301 ISGVTTLIFEGKPVGTPDAGAFWRIVAEHDVRVLFTAPTAFRAIRREDGDGELIARYNMP 360 Query: 357 CLKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAV 416 L+ ++LAGERADP+T+ WA+ L +PVIDHWWQTETGW IAANPLG+ LP K GSPA Sbjct: 361 NLRALFLAGERADPETLKWAERMLAIPVIDHWWQTETGWPIAANPLGLGALPVKHGSPAQ 420 Query: 417 PMPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYET 476 PMPGY V +LD+ GHPV G LG I ++LPLPPG LPTLW+A+DRF+ +YL FPGYY+T Sbjct: 421 PMPGYEVTVLDDAGHPVEAGTLGNIVIRLPLPPGCLPTLWHADDRFRSAYLDEFPGYYKT 480 Query: 477 GDAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQA 536 DAG DEDGYL+IM+RTDD+IN AGHRLSTGAMEEV A HPDVAECAVIGV D+LKGQA Sbjct: 481 ADAGYVDEDGYLFIMSRTDDIINCAGHRLSTGAMEEVCARHPDVAECAVIGVIDALKGQA 540 Query: 537 PVGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVN 596 P GFL L + A+VV ++R++IGPVAAFK A V+RLPKTRSGKILRGTM Sbjct: 541 PCGFLVLKRHVLRESTAIEAEVVAMIRDQIGPVAAFKTAITVNRLPKTRSGKILRGTMQK 600 Query: 597 IADGTDWKMPATIDDPAILDEITTALQGLGY 627 IADG WKMPATIDDPAIL+EI AL+ G+ Sbjct: 601 IADGIPWKMPATIDDPAILEEIAEALRKRGF 631 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: 1358 Number of extensions: 55 Number of successful extensions: 3 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: 636 Length adjustment: 38 Effective length of query: 591 Effective length of database: 598 Effective search space: 353418 Effective search space used: 353418 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