Align Lactate utilization protein B (characterized)
to candidate H281DRAFT_02904 H281DRAFT_02904 L-lactate dehydrogenase complex protein LldF
Query= SwissProt::Q81GA4 (473 letters) >FitnessBrowser__Burk376:H281DRAFT_02904 Length = 463 Score = 296 bits (757), Expect = 1e-84 Identities = 167/436 (38%), Positives = 245/436 (56%), Gaps = 18/436 (4%) Query: 42 ADELGNWEEWRELGEQIRQHTLENLDYYLMQLSENVSKRGGHVYFAKTKEEAAKYIQDVA 101 A + WE REL I++HTL +L YL Q + + G V++A T EE + + Sbjct: 38 AHGIAEWETLRELASGIKEHTLSHLSEYLEQFAASAEANGVVVHWAATAEEHNALVHKIM 97 Query: 102 KKKQAKKVVKSKSMVTEEISMNHALEEIGCEVLESDLGEYILQVDNDPPSHIIAPALHKN 161 ++ +VKSKSM+T+E M LE G V+E+DLGE I Q+D+ PSH++ PA+HK Sbjct: 98 SERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDHQDPSHMVVPAVHKL 157 Query: 162 RTQIRDVFKEKLGYE-NSDDPYEMTKFVRKQLREKFM-DAEIGVTGCNFAVANTGSLCLV 219 R + ++F +G + ++ D + + + R R F+ + G+TGCNFAVA TG++ + Sbjct: 158 RADVAELFGRTIGTDPHNSDIHYLAESQRMNTRPYFVREKTAGMTGCNFAVAETGTVVVC 217 Query: 220 TNEGNADLVMSIPKTQIAVMGMERMVPTMEELDVLVGLLCRSAVGQKLTSYVTVAGPIQE 279 TNEGNADL ++P IA +G+E+++P + +L V + +L RSA+G +T Y + Sbjct: 218 TNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGSPITQYTS-----HF 272 Query: 280 EEVDGPEEFHLVVVDNGRSQILG-SEFRSVLQCIRCAACVNVCPVYRHVGGHSYGSIYSG 338 E H ++VD+GRS+ L +F L+CIRC AC+N CPVYR GG SYG YSG Sbjct: 273 RAPRPGTEMHFILVDHGRSERLAMDDFWYSLKCIRCGACMNTCPVYRRSGGLSYGGTYSG 332 Query: 339 PIGAVLTPLLGGYDDYKELPYASSLCGACTEACPVKIPLHDLLLKHRQVIVEQEGRAPLA 398 PIGA++ P Y LP+AS+L G+CT CPVKI +H+ + K R VI E+ P Sbjct: 333 PIGAIINPTF-DLKRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRTVIAERH-EVPFV 390 Query: 399 EKLAMKMFSMGASSAALYKMGSKMAPAAMSPFTSGNRVSKGV--GPLKNWTDIREFPAPS 456 ++ +KM +S LY+ A+ R+ V PL W RE P Sbjct: 391 KQEVLKMAGRLLASPTLYRATVASMSGAL------RRLPNFVLYNPLNIWGRQRELPDAP 444 Query: 457 KERFRDWYKDHKKGGD 472 K+ F WYK ++ GGD Sbjct: 445 KQTFHAWYKQNRGGGD 460 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: 460 Number of extensions: 21 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: 463 Length adjustment: 33 Effective length of query: 440 Effective length of database: 430 Effective search space: 189200 Effective search space used: 189200 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