Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate CCNA_00021 CCNA_00021 putative aerobic-type carbon monoxide dehydrogenase, large subunit CoxL
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Caulo:CCNA_00021 Length = 730 Score = 342 bits (876), Expect = 5e-98 Identities = 254/731 (34%), Positives = 371/731 (50%), Gaps = 40/731 (5%) Query: 20 LASTAVG-ALVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVRLLSPFMEGGQGT 78 +AST VG AL++G A + A + E G P F++I PDG V ++S +E GQG Sbjct: 22 VASTMVGGALLVGCS---PADLMSAGSKVEVGAFGP-FIKIAPDGVVTVISKHIEFGQGN 77 Query: 79 HTAMAQIVGEELDADPATFIVEAAPPG-EAYVVMENGLRITGGSMSVRMSYPTMRRLGAL 137 H +A IV EELDAD + VE AP + Y G ++TGGS ++ S+ +R+ GA Sbjct: 78 HAGLAAIVAEELDADWSKVKVEQAPANAKLYANGNMGAQLTGGSSAISNSWDQLRKAGAG 137 Query: 138 ARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM-PVPDPASITLR 196 ARAM +QA A +W VPVGE+T + + H SG++ +GEL S A + P DP L+ Sbjct: 138 ARAMFVQAAANRWNVPVGEITVKDSVLAHT-SGKTAIFGELLSDAAKVNPPTDPK---LK 193 Query: 197 DPSQFRWIGKP-VKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQ 255 DP F IG V+R D+ KS G ALY+ D+++ +ML A V H PR G V S + ++ Sbjct: 194 DPKAFTLIGSDRVRRKDSQAKSDGTALYTQDVRLPDMLTAMVAHPPRFGGKVKSF-DATE 252 Query: 256 VEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPADFSSDKHR 315 + + GV V +P +AVVA+ + A+ EA++V+W E A+ R PA +R Sbjct: 253 AKKVAGVVEVFEIPTGIAVVAQNTYAARMGREALKVEWDEEKAEK--RGSPAIIQG--YR 308 Query: 316 EFLAAQQGPTRDD--ENEGDVAG--ALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPD 371 + L+ + + + + GD A KGA VE Y YL HA +EP + +A + + Sbjct: 309 DVLSGKDASVKWEPFDQRGDAAALETAKGADV-VELNYEFPYLAHATMEPMNCVAAVDGN 367 Query: 372 GTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALA 431 +++ +Q + + ++AK G P + + + GG FGR + S + + +A Sbjct: 368 -KVKLTFGSQGQTLDQLNVAKVVGCLPGSVEIETLFAGGSFGRRATFQSDYAV-ECVHIA 425 Query: 432 KAVS--RPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALAG 489 K V RP+KL+W+RE++ RP+ + + LD GLP A T+ + Sbjct: 426 KKVGKGRPVKLVWTREDDMRSGYFRPIVLHALKVKLDKDGLPAAWRHRIVTQSIMKGAPM 485 Query: 490 KQGDKIDPTAVEGLSGKSYAIPNKRI-AQIYVK--GAPMLGYWRSVGNSLNDFFYESFLD 546 G D +A EG++ Y + AQ+ G P+L +WRSVG + F E +D Sbjct: 486 PMGKGPDSSAFEGINDSPYLKATPVVDAQVAFPDIGVPVL-WWRSVGATHTAFVMEHTID 544 Query: 547 ELADKGGHDP--YELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMA 604 +LA K G DP Y ++ R +L A E K GP TR GVA+ Sbjct: 545 QLAAKAGKDPVAYRRAIYTKAGAERHLAVLNLALE-----KAGPKATAGWTR---GVAVH 596 Query: 605 SPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEA 664 FGS A IAEV +ENG +V + AID G ++P + AQ+ G GLS L E Sbjct: 597 ESFGSVVAQIAEVKLENGAPRVGRVVTAIDCGVAISPDQIAAQMEGGTCYGLSAALFGEV 656 Query: 665 VYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLT 724 DG+ N+D Y +L + V +V SG G+GEP P +APAVANA+ L Sbjct: 657 TLTDGQVDQTNFDGYRVLRINEAPSVETHIVPSGNPPSGVGEPGTPVIAPAVANALFALN 716 Query: 725 GQRVRSLPLSR 735 LP R Sbjct: 717 KAATSRLPFVR 727 Lambda K H 0.317 0.134 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: 1324 Number of extensions: 67 Number of successful extensions: 9 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: 739 Length of database: 730 Length adjustment: 40 Effective length of query: 699 Effective length of database: 690 Effective search space: 482310 Effective search space used: 482310 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:
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