Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate SMc03102 SMc03102 carbon monoxide dehydrogenase large subunit transmembrane protein
Query= metacyc::MONOMER-18071 (749 letters) >FitnessBrowser__Smeli:SMc03102 Length = 781 Score = 461 bits (1187), Expect = e-134 Identities = 282/779 (36%), Positives = 418/779 (53%), Gaps = 40/779 (5%) Query: 4 VGKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNGIVA 62 +G V R D +F+TG+ Y DD+ +P + YA FVRS + HA I+ ID + A + G++ Sbjct: 6 IGARVARKEDKRFLTGKGRYTDDMVVPGMKYAVFVRSPHAHATIRSIDATSAKSMPGVID 65 Query: 63 VFTAKEINPLLKGGIRP----WPTYI-DIRSFRYSERKAFPENKVKYVGEPVAIVLGQDK 117 V K+ LL GI W + D R + V+YVG+ VAIV+ Sbjct: 66 VLDGKQ---LLADGIGNLICGWMIHSKDGSPMRMGAWRPLAHETVRYVGDAVAIVVADSV 122 Query: 118 YSVRDAIDKVVVEYEPLKPVIRMEEA-EKDQVIIHEELKTNISYKIPF-KAGEVDKAFSE 175 RDA + VVV+YE L V +A + + IH E N+ + AG D+A + Sbjct: 123 AQARDAAEAVVVDYETLPVVTETLQALGEGEPQIHPEAPGNLIFDWELGDAGAADQAIAA 182 Query: 176 SDKVVRVEAINERLIPNPMEPRGIVSRFEAGT--LSIWYSTQVPHYMRSEFARILGI-PE 232 + V ++ IN RL PN MEPR + ++AG + + ++Q PH R + + PE Sbjct: 183 AAHVTELKIINNRLSPNAMEPRATLGIYDAGDDHFTCYTTSQNPHLARLVMSAFYNVAPE 242 Query: 233 SKIKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFT 291 +K++V PDVGG FG+K+ + PEE+ + +S G PV+WTA R+E L + R +V T Sbjct: 243 NKLRVIAPDVGGGFGSKIFIYPEEIVCLWASKRTGVPVKWTADRTEAFLTDAHGRDHVST 302 Query: 292 GEVAVKRDGTILGIKGKLLLDLGAYITVTAGIQPLII-PMMIPGPYKIRNLDIESVAVYT 350 ++A I +K + +LGAY+++ + P + ++ G Y I + VYT Sbjct: 303 VKMAFDSSNRITALKVDTIANLGAYMSLFSSCVPTYLYATLLSGQYAIPAIHANVRTVYT 362 Query: 351 NTPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTELPYTNPFGLRYDSG 410 NT P+ YRGA RPEATY++ER + T A ELG+ +R N + P+ P + YD+G Sbjct: 363 NTAPVDAYRGAGRPEATYLLERTIETAARELGISPAELRRINFIRTFPHQTPVIMNYDAG 422 Query: 411 DYVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP------------- 457 DY LR ++ + E ++G + G+G++ Y+E C P Sbjct: 423 DYEASLRGAMEAADWDGFAARKAEAERRGMKRGIGMSCYIEACGLAPSAAVGSLGAGVGL 482 Query: 458 WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASM 517 WE AEVRV+ G + V+TG+ HGQG ET AQ+VA+ + I V ++ GDTD V M Sbjct: 483 WESAEVRVNAVGTIEVMTGSHSHGQGHETTFAQVVAERFGVPIDSVNIVHGDTDKVQMGM 542 Query: 518 GTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSW 577 GTYGSRS +G SA K +K+ K KRIAA D ++ E G K+ + + W Sbjct: 543 GTYGSRSGAVGMSAVFKALDKVEAKAKRIAAHMMEADESDIVIEDGALKVAG-TDRSVPW 601 Query: 578 DDVASIAYRSH------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVLEYRAY 629 VA +Y +H +PGL E Y+ ++ TFP G +I VEVD +TG +++++ A Sbjct: 602 SQVALASYTAHNLPPGMEPGLKEGAFYDPSNFTFPAGCYICEVEVDPETGRTKIVQFVAA 661 Query: 630 DDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQLI-VTYADYYVPTAVEAPKFT 688 DD G ++NP + E Q+HGG Q +GQAL E +++GQL+ +Y DY +P A + P FT Sbjct: 662 DDFGNIINPLIVEGQVHGGLAQGIGQALLEGVHYDQSGQLLTASYMDYAMPRADDLPSFT 721 Query: 689 SVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAIGTRFTKTPTTPEEILRAIAS 747 ++ PSN P G KG GEA I P +I A+ DAIGT P TP+++ A+ S Sbjct: 722 VTTSNTPCPSN-PLGVKGCGEAGAIGSPPALINAITDAIGTNELTMPATPQKVWVAVHS 779 Lambda K H 0.317 0.136 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: 1332 Number of extensions: 63 Number of successful extensions: 11 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: 749 Length of database: 781 Length adjustment: 40 Effective length of query: 709 Effective length of database: 741 Effective search space: 525369 Effective search space used: 525369 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