Align Lactate utilization protein B (characterized)
to candidate 200690 SO1519 iron-sulfur cluster-binding protein (NCBI ptt file)
Query= SwissProt::Q81GA4 (473 letters) >FitnessBrowser__MR1:200690 Length = 464 Score = 297 bits (761), Expect = 4e-85 Identities = 164/444 (36%), Positives = 252/444 (56%), Gaps = 17/444 (3%) Query: 28 SSAQTRLYTNRLKAADELGNWEEWRELGEQIRQHTLENLDYYLMQLSENVSKRGGHVYFA 87 S A L R +AA L WE+ R+LG +I+ HTL NL YL +N G V++A Sbjct: 33 SKALWLLREKRDRAAGSLPEWEQLRQLGSEIKLHTLTNLAQYLETFEQNCLANGIKVHWA 92 Query: 88 KTKEEAAKYIQDVAKKKQAKKVVKSKSMVTEEISMNHALEEIGCEVLESDLGEYILQVDN 147 K E + + ++ + KK+VKSKSM+TEE +N LE+ G EV+++DLGE I+Q+ Sbjct: 93 KDGAEHNRIVHEILASHKVKKLVKSKSMLTEECHLNPYLEQRGIEVIDTDLGERIIQLAK 152 Query: 148 DPPSHIIAPALHKNRTQIRDVFKEKLGYE-NSDDPYEMTKFVRKQLREKFMDAEIGVTGC 206 PPSHI+ PA+H + ++ D+F +KLG + DP +T+ R LRE+F+ A+ +TG Sbjct: 153 MPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESDPLYLTRAARAHLREQFLSADAAMTGV 212 Query: 207 NFAVANTGSLCLVTNEGNADLVMSIPKTQIAVMGMERMVPTMEELDVLVGLLCRSAVGQK 266 N A+A+ G++ + TNEGNAD+ ++PK Q+ MG++++VP ++ VL+ L R+A GQ Sbjct: 213 NMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGIDKVVPDIDSAAVLLRTLARNATGQP 272 Query: 267 LTSY-VTVAGPIQEEEVDGPEEFHLVVVDNGRSQILGSE-FRSVLQCIRCAACVNVCPVY 324 +T+Y GP +VDG E H+++VDNGR++++ + L+CIRC C+N CPVY Sbjct: 273 VTTYSAFYRGP----QVDG--EMHVIIVDNGRTEMMKDKILAESLKCIRCGGCLNTCPVY 326 Query: 325 RHVGGHSYGSIYSGPIGAVLTPLLGGYDDYKELPYASSLCGACTEACPVKIPLHDLLLKH 384 R GG+SY GPIG + +D+ + +A +LCG+CT CP K+PL ++ H Sbjct: 327 RRSGGYSYNYTIPGPIGIAVG---ATHDNTNSIAWACTLCGSCTYVCPTKVPLDKIIHHH 383 Query: 385 RQVIVEQEGRAPLAEKLAMKMFSMGASSAALYKMGSKMAPAAMSPFTSGNRVSKGVGPLK 444 R++ E G+ P + M + +S L A A+ G+ + G Sbjct: 384 RRLKAE-AGKLPYGKNAYMPLVGKFMASTTLLNCSMGAARTALR-ILPGSLLKPFSGA-- 439 Query: 445 NWTDIREFPAPSKERFRDWYKDHK 468 W RE P F W+K H+ Sbjct: 440 -WGKYRELPVAPNSSFEAWFKKHR 462 Lambda K H 0.317 0.133 0.391 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: 500 Number of extensions: 17 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: 473 Length of database: 464 Length adjustment: 33 Effective length of query: 440 Effective length of database: 431 Effective search space: 189640 Effective search space used: 189640 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 (21.6 bits) S2: 51 (24.3 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