Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_084935382.1 HA51_RS14780 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_002095475.1:WP_084935382.1 Length = 366 Score = 228 bits (580), Expect = 2e-64 Identities = 129/326 (39%), Positives = 203/326 (62%), Gaps = 25/326 (7%) Query: 36 KLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGT 95 KL F +L L++ FF+ P+F+ V ++V +++ A+N LA+ T+VIIT+GIDLS+G Sbjct: 28 KLRTFIALFLIVGFFAITVPDFLAVGSMVIMVKHIAINAFLALGITFVIITAGIDLSIGA 87 Query: 96 MMTFCAVMAGVVLTNWGMPLPL-GIAA----------AIFFGALSGWISGMVIAKLKVPP 144 + C ++AG ++T G+ LP+ GIA + G L G +G +I K V P Sbjct: 88 TLGLCGMVAGWLITK-GIVLPMFGIAIFPSVWVIVPLVLVVGGLIGAANGWIITKYNVAP 146 Query: 145 FIATLGMMMLLKGLSLVISG--TRPIYFNDTE----GFSAIAQDSLIGDLIPSLPIPNAV 198 FI TLG M +L+G +++ SG T P + + GF I +G +P A+ Sbjct: 147 FICTLGTMYILRGTAMLTSGGETFPGLQGNPQLGNTGFDKIGAGYFLG-------LPWAI 199 Query: 199 LILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGL 258 ++ ++A+ + + + FGR +A+G NE A LSGVKV K+ VYT SG IAG+ Sbjct: 200 WMMVVLALVIAYVARRLPFGRQVYAIGDNERAAELSGVKVKSVKIWVYTISGFCAAIAGI 259 Query: 259 IIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMS 318 +++S+L ++ PA G +E++AIAAVV+GGTSL+GG GTILGT++GAF++ L +GL +M Sbjct: 260 VVSSQLVASHPANGTSFEMNAIAAVVLGGTSLAGGRGTILGTLVGAFVIGFLADGLIMMG 319 Query: 319 VAQEWQTVVTGVIIILAVYLDILRRR 344 V++ WQ V+ G++II+AV +D ++ R Sbjct: 320 VSEFWQMVIKGIVIIVAVIIDQMQSR 345 Lambda K H 0.326 0.139 0.398 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: 289 Number of extensions: 17 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: 347 Length of database: 366 Length adjustment: 29 Effective length of query: 318 Effective length of database: 337 Effective search space: 107166 Effective search space used: 107166 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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