Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate AZOBR_RS18175 AZOBR_RS18175 sugar ABC transporter
Query= uniprot:A8LLL5 (334 letters) >FitnessBrowser__azobra:AZOBR_RS18175 Length = 295 Score = 127 bits (320), Expect = 3e-34 Identities = 90/289 (31%), Positives = 150/289 (51%), Gaps = 16/289 (5%) Query: 53 PWIFLFPALFVLLLYLGYPVVETLRLSLLER--VPGGGYQWVGLDNYAQMASEPKFWEAM 110 P +F+ P LL++ GYP+V+ LS+ + G +VGLDNY ++ +P+F + + Sbjct: 8 PALFVAPVALYLLVFQGYPLVQEFLLSVTSTSLLSPGQQTYVGLDNYRELVFDPEFHQVL 67 Query: 111 RNNMFWLIVVPALSTAFGLLAAQLTDRIKWGN-VAKSIIFMPMAISFVGASVIWKLVYDG 169 R + +V S GLLAA L D G +A++++ +P A V A++I+ +++ Sbjct: 68 RVTAVYTLVCVVASIGLGLLAALLLDGTFRGRGIARALVTIPWAAPPVAAALIFVWMFNA 127 Query: 170 RPIEQEQIGILN--AIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRG 227 Q G+ + A +G V +L P + ++I +W F+ V++ AAL+G Sbjct: 128 ------QYGLFSHLAQFLGFAEGGVNWLDEPSFALPAILITTIWQIFPFSSVVILAALQG 181 Query: 228 IPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNG--QW 285 +P E EAA+IDGA L IF + P I P+V ++ IT+ L+ FD+++ MT G Sbjct: 182 VPSELREAAVIDGADRLSIFRAVTWPTIRPSVALLTLLITVWSLRRFDVIWLMTQGGPLG 241 Query: 286 ETQVLANYMFDKLFRANDWGVGSA---SAMVIMLLVTPILIWNIHSARK 331 ET L ++ + F D G +A +V+ +LVT + W A K Sbjct: 242 ETNTLVIDLYRRAFVYLDLGRAAAVGIIGLVVAILVTLVYFWLSTRAEK 290 Lambda K H 0.329 0.143 0.455 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: 260 Number of extensions: 14 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: 334 Length of database: 295 Length adjustment: 27 Effective length of query: 307 Effective length of database: 268 Effective search space: 82276 Effective search space used: 82276 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