Align Lactate utilization protein B (characterized)
to candidate Echvi_1568 Echvi_1568 Uncharacterized conserved protein containing a ferredoxin-like domain
Query= SwissProt::Q81GA4 (473 letters) >FitnessBrowser__Cola:Echvi_1568 Length = 457 Score = 305 bits (782), Expect = 2e-87 Identities = 163/438 (37%), Positives = 256/438 (58%), Gaps = 17/438 (3%) Query: 36 TNRLKAADELGNWEEWRELGEQIRQHTLENLDYYLMQLSENVSKRGGHVYFAKTKEEAAK 95 +NR ++A + WE R+ + + L +L L Q N G V +A+ +E + Sbjct: 32 SNRDRSAQGIPEWETLRDTASATKNYVLSHLGELLEQFEANAKANGVEVLWARDDKEHNE 91 Query: 96 YIQDVAKKKQAKKVVKSKSMVTEEISMNHALEEIGCEVLESDLGEYILQVDNDPPSHIIA 155 ++ + ++ + +VKSKS++TEE +NH LE+ G +V+++DLGE I+Q PSHI+ Sbjct: 92 HVYRILQENKVSNIVKSKSILTEECGLNHYLEKKGYDVVDTDLGERIIQFAKQTPSHIVL 151 Query: 156 PALHKNRTQIRDVFKEKLG-YENSDDPYEMTKFVRKQLREKFMDAEIGVTGCNFAVANTG 214 PA+H + I ++F + +G + + DP +T+ R+ LR+KF++A +TG NF +A TG Sbjct: 152 PAIHLKKQDIGEIFHDHIGTKKGASDPNYLTEAARQHLRKKFVEANAAITGVNFGIAETG 211 Query: 215 SLCLVTNEGNADLVMSIPKTQIAVMGMERMVPTMEELDVLVGLLCRSAVGQKLTSYVTVA 274 + TNEGNAD+ + IA MG+E+++P +L V + LL RSA GQ +T+Y + Sbjct: 212 GFVVCTNEGNADMGTHLADVHIACMGIEKLIPRAADLGVFLRLLARSATGQSITNYSS-- 269 Query: 275 GPIQEEEVDGPEEFHLVVVDNGRSQILGSE-FRSVLQCIRCAACVNVCPVYRHVGGHSYG 333 ++ ++++VDNGR+ LG E F++ L+CIRC AC+N CP+YR GGHSY Sbjct: 270 ---HFHRPAKGKKLYIILVDNGRTAQLGREDFKNSLKCIRCGACMNTCPIYRRSGGHSYN 326 Query: 334 SIYSGPIGAVLTPLLGGYD--DYKELPYASSLCGACTEACPVKIPLHDLLLKHRQVIVEQ 391 GPIG++L+P G D Y LP+AS+LCG+C++ CPVKI +H+ L K RQVI E Sbjct: 327 YTVPGPIGSILSP---GRDLKQYSTLPFASTLCGSCSDVCPVKINIHEQLYKWRQVITEN 383 Query: 392 EGRAPLAEKLAMKMFSMGASSAALYKMGSKMAPAAMSPFTSGNRVSKGVGPLKNWTDIRE 451 +++L+MK+ M LY + KMA A+ T + V L W R+ Sbjct: 384 T-NVDKSKQLSMKVAGMTFGKPVLYDLAGKMARTALK-ITPKSLV---YSSLNVWGKHRD 438 Query: 452 FPAPSKERFRDWYKDHKK 469 P KE F++W+K ++K Sbjct: 439 LPEVPKESFKEWFKKNRK 456 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: 485 Number of extensions: 24 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: 457 Length adjustment: 33 Effective length of query: 440 Effective length of database: 424 Effective search space: 186560 Effective search space used: 186560 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