Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate AO353_25120 AO353_25120 ABC transporter permease
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25120 Length = 320 Score = 139 bits (349), Expect = 1e-37 Identities = 97/312 (31%), Positives = 163/312 (52%), Gaps = 39/312 (12%) Query: 14 ERAKRRVDWVAYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQFVGLKNYEEL 73 +R + R W+ +L+P L+ + +++ P+ T + S T+ N FVGL NY L Sbjct: 22 QRRRVRAAWL---FLTPMLLCLALVAAWPLLRTFWFSLTDANLADTSGGSFVGLSNY--L 76 Query: 74 LNPHDPLSNLFLPTFIW-----TLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLL 128 + S + + W TL + + + L ++GL +A+LLN K R+L R L+ Sbjct: 77 FHDGSNWSGILVDPQWWNAVRNTLHFTVVSVGLEIVLGLLVALLLNIK-FTGRSLVRALI 135 Query: 129 IVPWAVPNLISMLAWQGLLNDQYGQINALLH--GVFGLPRIPWLTSALWARIAVIMVNVW 186 ++PWA+P ++S W +LNDQ+G IN L+ G+ P + W A + AVI+V+VW Sbjct: 136 LIPWAIPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAP-LAWTADADLSMWAVIIVDVW 194 Query: 187 AGFPYMMTVCLGALQSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSY-- 244 P++ + L ALQ +P+D YEAA +DG + +VF WR++LPLL+P+ Sbjct: 195 KTVPFVTLLMLAALQMLPSDCYEAARVDGIHPLKVF--------WRVTLPLLMPALLVAA 246 Query: 245 ------NFNNFNASYLLTGGGPPNSNNPFLGQTDILATAAYKMTLTFNRYDLGATISVLL 298 + F+ Y+LT NS++ T ++ A + + F G+ S LL Sbjct: 247 IFRILDSLRVFDVIYVLTS----NSSS-----TMSMSVYARQHLVEFQDVGYGSAASTLL 297 Query: 299 FILVALISWVQM 310 F++VA+I+ + + Sbjct: 298 FLVVAVIAMLYL 309 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: 318 Number of extensions: 16 Number of successful extensions: 5 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: 321 Length of database: 320 Length adjustment: 28 Effective length of query: 293 Effective length of database: 292 Effective search space: 85556 Effective search space used: 85556 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: 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