Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS01810 Length = 319 Score = 159 bits (401), Expect = 1e-43 Identities = 110/322 (34%), Positives = 169/322 (52%), Gaps = 34/322 (10%) Query: 2 IKRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGI 61 +K+NLP+++ + V+ + L ++ F S I + N+ +I+VGM FVI++GGI Sbjct: 1 MKKNLPILLALAALVV---FGLVRYEHFGSAYNITSFWRYNSMFALISVGMAFVIITGGI 57 Query: 62 DLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGC----AFGAFMGLLIDALKIPAF 117 DLSVG+V A V A L+ + + ++ GC A G GL+I LKI F Sbjct: 58 DLSVGTVAALASVVAA-------LTSVYGGWVAVLAGCGAGLAVGVLNGLIITRLKILPF 110 Query: 118 IITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGG---GRLSAM---GLLMLA 171 I+TLA GV+ L+ + D +S A G G L + G++ + Sbjct: 111 IVTLATSLGAHGVALLLGKN---------DAVSIAAESNFGNFGQGDLFGLPIPGIVAVV 161 Query: 172 VVVIGIFLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIY 231 V G TRFG AIGG+ +A LMG++ T + Y +S LA +AG++ + Sbjct: 162 AAVAGWLALRSTRFGRHSLAIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQ 221 Query: 232 TQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDG----- 286 AG GVG EL AI++VV+GGTLL+GG G++ T+ GV + GL+ +NF+ Sbjct: 222 FGAGQPNEGVGWELFAISAVVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFI 281 Query: 287 TLSSWWTKIAIGILLFIFIALQ 308 +LS++W + G+ L + I LQ Sbjct: 282 SLSAYWQSVIRGVFLLLVIVLQ 303 Lambda K H 0.329 0.145 0.428 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: 316 Number of extensions: 22 Number of successful extensions: 3 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: 331 Length of database: 319 Length adjustment: 28 Effective length of query: 303 Effective length of database: 291 Effective search space: 88173 Effective search space used: 88173 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 (21.8 bits) S2: 48 (23.1 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