Align Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate 3607411 Dshi_0825 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::Q9H6R3 (686 letters) >FitnessBrowser__Dino:3607411 Length = 630 Score = 694 bits (1790), Expect = 0.0 Identities = 328/622 (52%), Positives = 435/622 (69%), Gaps = 2/622 (0%) Query: 62 YKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHI 121 Y +AA DPE FW +AA+ I W P L + ++P WF + +N C+NAVDRH+ Sbjct: 3 YSQTYAAWKNDPEGFWMEAAQAIDWVTPPGAALNSDNAPLYEWFTDAEVNTCFNAVDRHV 62 Query: 122 ENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQA 181 + G GD++AII+DSPVT+TK TY E+ E+VS LAG L GI+KGD V+IYMPM+PQA Sbjct: 63 QAGNGDRVAIIHDSPVTHTKQEITYAELQERVSLLAGALRAKGIEKGDRVLIYMPMVPQA 122 Query: 182 MYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEA 241 + MLACAR+GAIHS++FGGFA+ EL+ RID PK ++ AS GIEPGR V Y PL++ A Sbjct: 123 LEAMLACARLGAIHSVVFGGFAANELAVRIDDATPKAIIAASCGIEPGRVVHYKPLLDGA 182 Query: 242 LKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSG 301 + + HKPD LI+ R E L PGRD DW E +CVPV HP YILYTSG Sbjct: 183 IDLATHKPDFCLIFQR-EQEVAHLEPGRDFDWHEAQYGVDPAECVPVAGNHPAYILYTSG 241 Query: 302 TTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNT 361 TTG PKGV+RPT G+ V L+W+M +IY + PG+V+WAASD+GWVVGHSYICY PL+HGNT Sbjct: 242 TTGQPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYAPLIHGNT 301 Query: 362 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 421 T+++EGKPVGTPDAG ++RV++EH V + FTAPTA+RA++++DP +Y L+ KT+ Sbjct: 302 TIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTALRAVKREDPNGEFIGKYDLSHLKTV 361 Query: 422 FVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVPG 481 ++AGER D +T++W+ + VPV+DHWWQTETG I A+ +G+ + G ++PG Sbjct: 362 YLAGERADPDTIQWTMDKLGVPVIDHWWQTETGWAIAANPMGIEHLPV-KIGSPSVAMPG 420 Query: 482 YNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 541 Y+V +LD+ + LG I VKLPL PG LW+ +E F Y FPGYY+T DAG Sbjct: 421 YDVQVLDEGGHPVAPGTLGAIAVKLPLAPGTLPNLWQAEERFVKSYLTTFPGYYETGDAG 480 Query: 542 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLAL 601 Y+DE+GYLY+M+R DDVINVAGHR+S GA+EE + SH VA+CAV+G D LKG +PL Sbjct: 481 YIDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGF 540 Query: 602 CVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVNG 661 L +N +++ +E VK VR+ IGPVAAF+ A V +LPKTRSGKI R + I +G Sbjct: 541 LCLSAGVNRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600 Query: 662 KPYKITSTIEDPSIFGHVEEML 683 P+K+ +TI+DP+I + E L Sbjct: 601 TPWKMPATIDDPAILDEITEAL 622 Lambda K H 0.318 0.136 0.422 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: 1388 Number of extensions: 68 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: 686 Length of database: 630 Length adjustment: 38 Effective length of query: 648 Effective length of database: 592 Effective search space: 383616 Effective search space used: 383616 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