Align Lactate utilization protein B (characterized)
to candidate 14445 b0307 predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain (NCBI)
Query= SwissProt::Q81GA4 (473 letters) >FitnessBrowser__Keio:14445 Length = 475 Score = 565 bits (1455), Expect = e-165 Identities = 270/469 (57%), Positives = 345/469 (73%), Gaps = 2/469 (0%) Query: 1 MSMKISEKKFNDRVGDGIQDSFMRGAVSSAQTRLYTNRLKAADELGNWEEWRELGEQIRQ 60 MS+K S F R+ I+D MR AV++AQ R+ NR K DELG+WEEWR+ QIR Sbjct: 1 MSIKTSNTDFKTRIRQQIEDPIMRKAVANAQQRIGANRQKMVDELGHWEEWRDRAAQIRD 60 Query: 61 HTLENLDYYLMQLSENVSKRGGHVYFAKTKEEAAKYIQDVAKKKQAKKVVKSKSMVTEEI 120 H L NLD YL QLSE V++ GGHVYFA+TKE+A +YI VA++K A+KVVKSKSMVTEEI Sbjct: 61 HVLSNLDAYLYQLSEKVTQNGGHVYFARTKEDATRYILQVAQRKNARKVVKSKSMVTEEI 120 Query: 121 SMNHALEEIGCEVLESDLGEYILQVDNDPPSHIIAPALHKNRTQIRDVFKEKLGYENSDD 180 +NH L++ G +V+E+DLGEYILQ+D DPPSH++ PA+HK+R QIR V E+LGYE + Sbjct: 121 GVNHVLQDAGIQVIETDLGEYILQLDQDPPSHVVVPAIHKDRHQIRRVLHERLGYEGPET 180 Query: 181 PYEMTKFVRKQLREKFMDAEIGVTGCNFAVANTGSLCLVTNEGNADLVMSIPKTQIAVMG 240 P MT F+R+++RE F+ AEIG+TGCNFAVA TGS+CLVTNEGNA + ++PKT IAVMG Sbjct: 181 PEAMTLFIRQKIREDFLSAEIGITGCNFAVAETGSVCLVTNEGNARMCTTLPKTHIAVMG 240 Query: 241 MERMVPTMEELDVLVGLLCRSAVGQKLTSYVT-VAGPIQEEEVDGPEEFHLVVVDNGRSQ 299 MER+ PT E+DVL+ +L RSAVG +LT Y T + GP + VDGPEEFHLV+VDNGRS+ Sbjct: 241 MERIAPTFAEVDVLITMLARSAVGARLTGYNTWLTGPREAGHVDGPEEFHLVIVDNGRSE 300 Query: 300 ILGSEFRSVLQCIRCAACVNVCPVYRHVGGHSYGSIYSGPIGAVLTPLLGGYDDYKELPY 359 +L SEFR VL+CIRC AC+N CP YRH+GGH YGSIY GPIGAV++PLLGGY D+K+LPY Sbjct: 301 VLASEFRDVLRCIRCGACMNTCPAYRHIGGHGYGSIYPGPIGAVISPLLGGYKDFKDLPY 360 Query: 360 ASSLCGACTEACPVKIPLHDLLLKHRQVIVEQEGRAPLAEKLAMKMFSMGASSAALYKMG 419 A SLC AC CPV+IPL L+L+HR+V+ E +G AE+ A+KMF+ S L+K+G Sbjct: 361 ACSLCTACDNVCPVRIPLSKLILRHRRVMAE-KGITAKAEQRAIKMFAYANSHPGLWKVG 419 Query: 420 SKMAPAAMSPFTSGNRVSKGVGPLKNWTDIREFPAPSKERFRDWYKDHK 468 A S F +G + G + +W + R+ P E FR W+K H+ Sbjct: 420 MMAGAHAASWFINGGKTPLKFGAISDWMEARDLPEADGESFRSWFKKHQ 468 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: 673 Number of extensions: 22 Number of successful extensions: 5 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: 475 Length adjustment: 33 Effective length of query: 440 Effective length of database: 442 Effective search space: 194480 Effective search space used: 194480 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