Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011427294.1 RHE_RS21035 propionyl-CoA synthetase
Query= BRENDA::A0A0G2K047 (683 letters) >NCBI__GCF_000092045.1:WP_011427294.1 Length = 636 Score = 660 bits (1703), Expect = 0.0 Identities = 321/630 (50%), Positives = 434/630 (68%), Gaps = 12/630 (1%) Query: 58 YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTS----WFVEGMLNICYNAI 113 Y +AA +DPE FW +AA I W+KP E Y P WF N C+N + Sbjct: 5 YHQTYAAWKSDPEAFWREAAADIDWFKP----PERVYSPDEGIYGRWFSGAETNTCHNCL 60 Query: 114 DRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPM 173 DRH+ G+G + AII+DS +T K SY EVL +V +A L+ G+ +GD V++YMPM Sbjct: 61 DRHVRAGRGGETAIIFDSAMTGEKRRFSYDEVLGEVKAIAETLLALGIARGDRVILYMPM 120 Query: 174 IPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPL 233 +PQA+++MLACARIGA+HS++FGGFA+ EL+ RID ++V+TAS G+EPGR V Y PL Sbjct: 121 LPQAVFSMLACARIGAVHSVVFGGFAASELAARIDDSGARLVITASCGLEPGRVVAYKPL 180 Query: 234 LEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHD--CVPVLSEHPLY 291 +++A+ I + KP+R L+ RP + + L+ GRD D+E +A + + CV V + PLY Sbjct: 181 VDQAIEIARMKPERCLVLQRPQL-RAELVGGRDEDFEAAVAPHRGAEVACVSVRATDPLY 239 Query: 292 ILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGP 351 ILYTSGTTG PKGVVR GG+ V LNW+M +IYGLKPGEV+W ASD+GWVVGHSYI Y P Sbjct: 240 ILYTSGTTGQPKGVVRDNGGHMVALNWSMRNIYGLKPGEVFWTASDIGWVVGHSYIVYAP 299 Query: 352 LLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSL 411 L+ G TT+++EGKPVGTPDAGA++R++AEH V LFTAPTA RAIR++D L +Y++ Sbjct: 300 LISGVTTLIFEGKPVGTPDAGAFWRIVAEHDVRVLFTAPTAFRAIRREDGDGELIARYNM 359 Query: 412 TRFKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQA 471 + LF+AGER D ETL+W++++ +PV+DHWWQTETG PI A+ +GLG + G Sbjct: 360 PNLRALFLAGERADPETLKWAERMLAIPVIDHWWQTETGWPIAANPLGLG-ALPVKHGSP 418 Query: 472 GKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYY 531 + +PGY V +LDD ++A +LGNIV++LPLPPG LW + F+ Y ++FPGYY Sbjct: 419 AQPMPGYEVTVLDDAGHPVEAGTLGNIVIRLPLPPGCLPTLWHADDRFRSAYLDEFPGYY 478 Query: 532 DTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKG 591 T DAGY+DE+GYL++MSR DD+IN AGHR+S GA+EE H V +CAV+G D LKG Sbjct: 479 KTADAGYVDEDGYLFIMSRTDDIINCAGHRLSTGAMEEVCARHPDVAECAVIGVIDALKG 538 Query: 592 HVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTL 651 P VLK+ V + E+V +R IGPVAAF+ A+ V +LPKTRSGKI R T+ Sbjct: 539 QAPCGFLVLKRHVLRESTAIEAEVVAMIRDQIGPVAAFKTAITVNRLPKTRSGKILRGTM 598 Query: 652 SALVNGKPYKVTPTIEDPSIFGHIEEVLKQ 681 + +G P+K+ TI+DP+I I E L++ Sbjct: 599 QKIADGIPWKMPATIDDPAILEEIAEALRK 628 Lambda K H 0.318 0.136 0.421 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: 1291 Number of extensions: 64 Number of successful extensions: 4 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: 683 Length of database: 636 Length adjustment: 38 Effective length of query: 645 Effective length of database: 598 Effective search space: 385710 Effective search space used: 385710 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