Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate 18061 b4033 maltose transporter subunit (NCBI)
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Keio:18061 Length = 514 Score = 181 bits (460), Expect = 3e-50 Identities = 97/252 (38%), Positives = 152/252 (60%), Gaps = 6/252 (2%) Query: 66 GLKNYEELLNPHDPLSNLFLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYR 125 G KN+ + + + FL F+WT+V++L T L VG+ LA L+ + +R + +YR Sbjct: 260 GWKNFTRVFTD-EGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYR 318 Query: 126 TLLIVPWAVPNLISMLAWQGLLNDQYGQINALLHGVFGLPRIPWLTSALWARIAVIMVNV 185 LLI+P+AVP+ IS+L ++GL N +G+IN +L +FG+ + W + AR +I+VN Sbjct: 319 VLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGV-KPAWFSDPTTARTMLIIVNT 377 Query: 186 WAGFPYMMTVCLGALQSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYN 245 W G+PYMM +C+G L++IP D YEA+ +DGA +Q F +T+P + + PL+I SF++N Sbjct: 378 WLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFN 437 Query: 246 FNNFNASYLLTGGGPPN-SNNPFLGQTDILATAAYKMTLT---FNRYDLGATISVLLFIL 301 FNNF LLT GGP G TD+L Y++ + L A I+ L+F+L Sbjct: 438 FNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIATLIFLL 497 Query: 302 VALISWVQMRYT 313 V ++ V ++ T Sbjct: 498 VGALAIVNLKAT 509 Score = 28.5 bits (62), Expect = 4e-04 Identities = 11/40 (27%), Positives = 25/40 (62%) Query: 24 AYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQ 63 A+ Y+ P + + + + P+ TI I+FTN++ + L+++ Sbjct: 64 AWRYVYPGMAGMGLFVLFPLVCTIAIAFTNYSSTNQLTFE 103 Lambda K H 0.327 0.140 0.451 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: 457 Number of extensions: 29 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 321 Length of database: 514 Length adjustment: 31 Effective length of query: 290 Effective length of database: 483 Effective search space: 140070 Effective search space used: 140070 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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