Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= SwissProt::O51924 (295 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 140 bits (353), Expect = 4e-38 Identities = 91/258 (35%), Positives = 134/258 (51%), Gaps = 4/258 (1%) Query: 21 ILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFV---GLRNYLRVLSAREFWYSTFV 77 +LP L V+ +LP + +SL P F L NY +L F S + Sbjct: 30 LLPALVVLGGITLLPGLFLLGVSLTPLSLVNPGTVFDFSDPLGNYRELLRDARFHNSVLL 89 Query: 78 TVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELMYNYSY 137 + S SV L+ GL AL+LN R + +RA LIP +P I+ A W+++Y Sbjct: 90 QLHLSATSVGLQLAAGLGVALLLNVRARFFEAIRAAFLIPMVLPPIVVALIWKILYTPDV 149 Query: 138 GLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAIPQDLYEAAL 197 + +L G+ + + P A +AI +A+ W+ PF L++LA LQ IP + EAA Sbjct: 150 SPLHRLLEEAGLPVDSLITDPTLAIWAIAVAETWQWFPFTMLMVLATLQLIPDEPLEAAR 209 Query: 198 IDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSISLLAF 257 IDGA+ + F+ I L L+P L+V + R ID+L+ F +IYVLT GGPG AT + F Sbjct: 210 IDGANRRQVFRHIILAYLRPALVVCGLFRLIDSLKAFPLIYVLTNGGPGTATEVTNYYGF 269 Query: 258 -NYYNLGDYGIGSAISIL 274 +N +G SAI++L Sbjct: 270 IEAFNFSYWGYASAIAVL 287 Lambda K H 0.329 0.145 0.439 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: 278 Number of extensions: 14 Number of successful extensions: 1 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: 295 Length of database: 310 Length adjustment: 27 Effective length of query: 268 Effective length of database: 283 Effective search space: 75844 Effective search space used: 75844 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