Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate BPHYT_RS32805 BPHYT_RS32805 acylaldehyde oxidase
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__BFirm:BPHYT_RS32805 Length = 756 Score = 389 bits (999), Expect = e-112 Identities = 277/772 (35%), Positives = 394/772 (51%), Gaps = 72/772 (9%) Query: 14 LSRRRFL--ASTAVGALVIGFG-LPLGAGRVQAATSAERGTQVP--AFLEIRPDGTVRLL 68 L RR FL + AVGALV+G+ LP G + +G+QV +++I D +V ++ Sbjct: 2 LKRRTFLLGGAGAVGALVVGWSVLPPGQRLTTSMPLPAQGSQVALNGWVKIAADNSVTIM 61 Query: 69 SPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAY-------------------- 108 E GQG HT +A ++ EELDAD + VE +P + Y Sbjct: 62 MCKAEMGQGIHTGLAMLLAEELDADWSQVRVEDSPIDKIYNSVQSIIDDLPFRPDDDSTV 121 Query: 109 ----------VVMENGLRITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELT 158 +V E G +TGGS S+ + MR GA ARAML+ A A QW VP GE Sbjct: 122 KRTTVWMTRKLVREAGTMMTGGSSSINDLWTPMREAGASARAMLIGAAAAQWKVPPGECR 181 Query: 159 TQPGRVVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKST 218 + G+V+H SG +GEL+S A +P +TL+DP+ F+ IGKP++R++A K Sbjct: 182 AEGGQVLHP-SGHKASFGELSSMAAQQALP--RKVTLKDPANFKLIGKPLRRIEAASKIN 238 Query: 219 GKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLP-----GAVA 273 G A + ID+ D +L+A+V+ P LG +V + + + + V P G VA Sbjct: 239 GTARFGIDVLPDGLLYASVEMCPTLGGSVAKFDATAAGKMPGFIKAFAVAPYNGGTGGVA 298 Query: 274 VVAERWWHAKRAVEAIQVDWQEAAA------DSALRVMPADFSSDKHREFLAAQQGPTRD 327 V+A+ + A AV A+ V W + A D+ R+ A +D H + Sbjct: 299 VIADNPFRAMNAVAAVDVTWHDGPAAKLSNADADRRLAQALDDNDGHAYY---------- 348 Query: 328 DENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFR 387 + GDV AL A V A Y YL H +EP + + DG +W+ Q P + R Sbjct: 349 --HLGDVDAALTRAARTVSAEYRAPYLAHGAVEPLNCTVQV-ADGAATVWVSTQMPGLAR 405 Query: 388 ADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAK-AVSRPIKLIWSREE 446 +AK LD ++ + + LLGG FGR D QA A+A+ RP++ +WSR + Sbjct: 406 HHVAKVLDLDADKVDVQTFLLGGAFGRRLELDFI---AQAAAIAREGGGRPVQTLWSRAQ 462 Query: 447 EFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPT-EALAGKQGDK---IDPTAVEG 502 +F D RP + + +A D+ G VA +A SA++ EALA G ID T EG Sbjct: 463 DFTHDFYRPACLSRLKAGFDNDGKLVAWQAASASQAIVPEALARYYGAPRLPIDKTTCEG 522 Query: 503 LSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLH 562 + Y P R+A V+ +G+WRSVG+S FF E F DELA G DP R Sbjct: 523 AFDQPYEWPAARVAHKIVELPVPVGFWRSVGHSHQAFFTEGFTDELAVATGKDPIAFRAA 582 Query: 563 LLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENG 622 LL +PR +L+ A LS W+ A DG RARGVA+ FGS A +AEVSI G Sbjct: 583 LLEQHPRHLAVLKRAAALSD-WEHPLTHAADGAPRARGVALHEAFGSVVAQVAEVSIGPG 641 Query: 623 K-VKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPI 681 K ++VH + ID G VNP ++ Q+ AV GLS L +E V+G+ + +N+ +P+ Sbjct: 642 KKIRVHRVVCVIDCGIPVNPNLIRQQMESAVVFGLSAALQDEITLVNGQVQQKNFLDFPV 701 Query: 682 LAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733 + + ++ S G+GE +P VAPAVANAV +LTGQR+RSLPL Sbjct: 702 VRIDDCPVIDTDIMPSQLHPQGVGEAGVPPVAPAVANAVFKLTGQRLRSLPL 753 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: 1379 Number of extensions: 72 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 756 Length adjustment: 40 Effective length of query: 699 Effective length of database: 716 Effective search space: 500484 Effective search space used: 500484 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