Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate 352309 BT2782 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__Btheta:352309 Length = 549 Score = 146 bits (369), Expect = 2e-39 Identities = 144/553 (26%), Positives = 226/553 (40%), Gaps = 53/553 (9%) Query: 27 FLDRAAVVHPTRKSVIHGSRE--YTWRQTYDRCRRLASALADRSIGPGSTVAIIAPNIPA 84 +L+ A P ++ +++ R +TW Q R +A L + G+ V I A N+P Sbjct: 11 WLEHWAEETPDKEYIVYSDRNLRFTWSQLNQRVDDMAKGLIAVGVERGTHVGIWAANVPD 70 Query: 85 MYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMV-----DQEFFTLAEDSLRL 139 + GAV VN + +L +S + + D +F + L Sbjct: 71 WLTLLYACAKIGAVYVTVNTNYKQAELEYLCQNSDMHTLCIVNGEKDSDFVQMTYTMLPE 130 Query: 140 MEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATG-----DPNYPWQPPA 194 ++ K + + + +R + A + L G D + Sbjct: 131 LKTCERGHLKSERFPYMKNVIYVGQEKHRGMYNTA----EILLLGNNVEDDRLTELKSKV 186 Query: 195 DEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWT--------LP 246 D + + YTSGTT PKGV+L H Y +A + G G +T +P Sbjct: 187 DCHDVVNMQYTSGTTGFPKGVMLTH---YNIANN-----GFLTGEHMKFTADDKLCCCVP 238 Query: 247 MFHCNGWCFPWSLAVLSG-TSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKE 305 +FHC G + G T + + + V + I K + T P + A ++ P Sbjct: 239 LFHCFGVVLATMNCLTHGCTQVMVERFDPLVVLASIHKERCTALYGVPTMFIAELHHPMF 298 Query: 306 DTILPLPHTVHVMTAGAAPPPSVLFSMNQKGF-RVAHTYGLSETYGPSTVCAWKPEWDSL 364 D +M AG+ P ++ + +K + +V YGL+E T +D Sbjct: 299 DLFDMSCLRTGIM-AGSLCPVELMKQVEEKMYMKVTSVYGLTEAAPGMTATRIDDSFD-- 355 Query: 365 PPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEA 424 + R ++ VID +TG+ P GE+ RG MKGY KNPEA Sbjct: 356 -------VRCNTVGRDFEFTEVRVIDPETGEECPVG--VQGEMCNRGYNTMKGYYKNPEA 406 Query: 425 NKETF-AGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEA 483 E + HSGD+ +K D I R KD+II GGENI E+E +Y V + Sbjct: 407 TAEVIDKDNFLHSGDLGIKDEDGNYRITGRIKDMIIRGGENIYPREIEEFLYKLDGVKDV 466 Query: 484 SVVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVF-GPLP 542 V P +++ E+ AF+ L+ E H+ D+ FC+ K+ Y +PK V F P Sbjct: 467 QVAGIPSKKYGEAVGAFIILQEGVEMHE-----SDVRDFCKNKISRYKIPKYVFFVKEFP 521 Query: 543 KTATGKIQKHILR 555 T +GKIQK L+ Sbjct: 522 MTGSGKIQKFRLK 534 Lambda K H 0.319 0.134 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: 644 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 569 Length of database: 549 Length adjustment: 36 Effective length of query: 533 Effective length of database: 513 Effective search space: 273429 Effective search space used: 273429 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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