Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__azobra:AZOBR_RS27940 Length = 329 Score = 145 bits (367), Expect = 1e-39 Identities = 104/313 (33%), Positives = 159/313 (50%), Gaps = 16/313 (5%) Query: 7 PLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVG 66 P + + VLG + P F S I N+LT AF+GIIAVG TFVI +GGIDLSVG Sbjct: 19 PFLALAALIVLGTIVN----PVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGGIDLSVG 74 Query: 67 SVIAFTG----VFLAKVIGDFGLSP---LLAFPLVLVMGCAFGAFMGLLIDALKIPAFII 119 S+ AF V + ++G G L+ + L +G G GLL+ ++ AFI+ Sbjct: 75 SLAAFASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEAFIV 134 Query: 120 TLAGMFFLRG-VSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVV-VIGI 177 TL M R V+Y+ ++ +N I + + GG + +L AVV +IG Sbjct: 135 TLGTMGIFRSLVTYIADGGTLSLNSEIRTIYRPVYY---GGVFGISYPILAFAVVALIGA 191 Query: 178 FLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYA 237 + +RTRFG AIG + A I+ + ++L +A +++ + A Sbjct: 192 LIMYRTRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASA 251 Query: 238 LAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAI 297 G+ EL+AIA+V+IGGT+L GG G + GT+ G + LI +N G +S + Sbjct: 252 TTGLLWELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQ 311 Query: 298 GILLFIFIALQRG 310 G+++ + + LQRG Sbjct: 312 GVIIIVAVLLQRG 324 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: 329 Number of extensions: 19 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 303 Effective length of database: 301 Effective search space: 91203 Effective search space used: 91203 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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