Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate AZOBR_RS21105 AZOBR_RS21105 acetyl-CoA carboxylase
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__azobra:AZOBR_RS21105 Length = 666 Score = 504 bits (1298), Expect = e-147 Identities = 307/679 (45%), Positives = 400/679 (58%), Gaps = 53/679 (7%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 +FSK+LIANRGEIACR+IRTARRLGI+TVAVYSDAD +ALHV +ADEA+ IG AP+A+SY Sbjct: 1 LFSKILIANRGEIACRVIRTARRLGIKTVAVYSDADRNALHVEMADEAVHIGAAPSAQSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L IV A + GAQA+HPGYGFLSE +F EA+A AG+ F+GP AI+AMG K +K Sbjct: 61 LLIDRIVDACKKTGAQAVHPGYGFLSEKREFQEALAAAGIAFIGPDAHAIQAMGDKIESK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 L + +GV VPGY G D S AR+IGYPV+IKA AGGGGKGMR E+ Sbjct: 121 KLAKAAGVSTVPGYLGVIADDSEAVTIARDIGYPVMIKASAGGGGKGMRVAWNDEEAREG 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 +A+ EA S+F D V +E+Y+ +PRHIE+QV D G ++L ER+CS+QRRHQKVIE Sbjct: 181 FRSAQNEARSSFADDRVFVEKYIQQPRHIEIQVLADGQGTALYLGERECSIQRRHQKVIE 240 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAP+P + A R+AMG+ AV A+A+ Y AGTVEFI D +FYF+EMNTRLQV Sbjct: 241 EAPSPFLDAATRKAMGEQAVALARAVDYKSAGTVEFIVDAER-----NFYFLEMNTRLQV 295 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTE +TG+DLVE +RVA+GE L KQ DI ++GWA E+R+YAEDP R FLP+TGRL Sbjct: 296 EHPVTELVTGLDLVELMIRVAAGEKLTLKQEDIHLHGWAIESRVYAEDPFRNFLPSTGRL 355 Query: 361 TELSFP--EGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGG 418 T P + RVD+GV +G I+ YYDP+IAKL G R AA+ R+++AL + I G Sbjct: 356 THYRPPSEDPHVRVDTGVYEGGEISMYYDPMIAKLCSWGSTRDAAIARMREALDQYYIRG 415 Query: 419 TVTNRDFLIRLTEEHDFRSGHPDTGLIDREIER-LTAPVAPGDEALALAAIFS------- 470 N FL L F G T I E A P +E L A+ + Sbjct: 416 VSHNIPFLASLMANQRFVEGRLTTNFIAEEYPTGFHASDLPPEEPAVLIAVAAVIHRCLN 475 Query: 471 ------TGALDPN--RSTDPWSSLGSWQIWGDAHRMVV--IEHADVRATVTLASRGR--- 517 +G + N R D W + + G H + V + + R T+ GR Sbjct: 476 DRDIQISGKMPGNKVRVRDDWVVV----MDGTQHPVHVRPTDGSPQRIGYTVDFEGRHHV 531 Query: 518 -------DQFAVRAGASTLPVLV-LDRFEGGARLEVAGQKRLIRFSRDREALTLFHGGRN 569 Q R + V V +DR G RL +G + L++ A Sbjct: 532 VWSDWTLGQPLFRGTVNGAHVCVQVDRVGVGYRLSHSGSQALVKVLTPNAARL------- 584 Query: 570 LVFHVPDGLTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLS 629 D L ++ L++PMPGL+ V V G V G+ L V+EAMKME L Sbjct: 585 ------DALMPVKAPPDMSKFLLSPMPGLLVSVAVTEGQEVKAGEVLAVVEAMKMENILR 638 Query: 630 ASREGTIANVHVAEGAQVS 648 A+++GT++ VH G+ ++ Sbjct: 639 AAQDGTVSKVHATPGSSLA 657 Lambda K H 0.319 0.135 0.394 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: 1133 Number of extensions: 52 Number of successful extensions: 4 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: 662 Length of database: 666 Length adjustment: 38 Effective length of query: 624 Effective length of database: 628 Effective search space: 391872 Effective search space used: 391872 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: 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