Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 199218 SO0021 fatty oxidation complex, alpha subunit (NCBI ptt file)
Query= metacyc::MONOMER-20678 (699 letters) >lcl|FitnessBrowser__MR1:199218 SO0021 fatty oxidation complex, alpha subunit (NCBI ptt file) Length = 716 Score = 346 bits (888), Expect = 2e-99 Identities = 239/680 (35%), Positives = 344/680 (50%), Gaps = 27/680 (3%) Query: 10 QDQVAIVTVDSP-PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68 +D +A + ++P VN + +++ +QA+VL TFI GADITEF Sbjct: 14 EDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSGKDTFIVGADITEF 73 Query: 69 -GKPPQPPAL--------NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119 G Q A+ N V LE+ P PT +AI G ALGGG E L FR+A A Sbjct: 74 LGLFAQDDAVLLSWVEQANAVFNKLEDLPFPTASAIKGFALGGGCETILATDFRIADTTA 133 Query: 120 KLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENL 177 K+GLPE KLG++PG GGT RLPR +G + A++ I G+ A +ALK G V+ VV E L Sbjct: 134 KIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGNEQRAEDALKVGAVDAVVAPEAL 193 Query: 178 VAGAVAFAKKVLAEKRPLRRLRDDD-SKLAAAKADRSIFTNAVAAMTKKARGLE--APFA 234 A+ K +AEK + R S L K + + M G AP A Sbjct: 194 EVAAIQMLKDAVAEKLDWQARRQRKLSPLTLPKLEAMMSFTTAKGMVFSVAGKHYPAPMA 253 Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294 + + A + L+ E + F+KL +D +KA F + K G + Sbjct: 254 AVNVVEQAATKGRSDALQIEHQAFIKLAKTDVAKAL-IGIFLNDQFVKGKAKKAGKLAKA 312 Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354 V+ A++GAG MGGGIA A+ G P+ + + + L GL K A ARG P+ Sbjct: 313 VNSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLNEAAKLLSAQVARGRSTPE 372 Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414 AK + IT + VK AD+++EAV E VK +V V+ + A++ASNTS +S Sbjct: 373 KMAKVLNNITPALEYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSEDAIIASNTSTIS 432 Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474 I +A + K+P+ GMHFF+P + M L E++RG ++ + + + V+ A K+ K P+VV Sbjct: 433 ISLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAYASKMGKTPIVVN 492 Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLDIGWRS 533 C GF NR+L LL EG +D V+ K FG PMGP + D+ GLD G + Sbjct: 493 DCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYLLDVVGLDTGHHA 552 Query: 534 R-------KDRGIKS--EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDT 584 + DR KS + D + E R GQK GKG+Y Y SR P +V+ + Sbjct: 553 QAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRG-KPKKDVDPTSYEL 611 Query: 585 LAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGP 644 L +++ +EI+ R + PMI E R LEE I A P++ D+ +YG G+P +RGG Sbjct: 612 LKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYGLGFPPFRGGV 671 Query: 645 MHYADSVGLKHIAERLSAYA 664 Y D++G+ + YA Sbjct: 672 FRYLDTMGVANFVALADKYA 691 Lambda K H 0.317 0.134 0.383 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: 1059 Number of extensions: 57 Number of successful extensions: 7 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: 699 Length of database: 716 Length adjustment: 39 Effective length of query: 660 Effective length of database: 677 Effective search space: 446820 Effective search space used: 446820 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: 55 (25.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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