Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 301 bits (770), Expect = 2e-86 Identities = 172/355 (48%), Positives = 227/355 (63%), Gaps = 18/355 (5%) Query: 1 MAKIQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59 MA + ++K++ G ADVL G++LDI GEF VLVGPSGCGKSTLLR L GLE G Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 60 ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119 ++I G+ +N + P R IAMVFQSYALYPHM V +NM FGLK+ + ++I R+ + Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 +L+I HLL R P+ELSGGQRQRVA+GRA+ RQ + LFDEPLSNLDA LR Q RLEI +L Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239 H +T++YVTHDQ+EA TLGD+I V+ +G I+Q GTP E+Y +P+N F+A FIGSP+M Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240 Query: 240 NFLEGAVLE--------KIPWPEARKAD-QILGIRPDAFALNQGPLGTQ-EVALGDFQ-- 287 NF +G V +I AD LG+ P A A+ G Q LGD Q Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGA-AVTLGLRAEQIREGLGDGQPL 299 Query: 288 ---IDISENLGGQQMLHGTL-AGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFD 338 +++ E+LG L+ TL G+++ + D N + Q + L + HLFD Sbjct: 300 HGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFD 354 Lambda K H 0.318 0.136 0.383 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: 355 Number of extensions: 15 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: 347 Length of database: 377 Length adjustment: 29 Effective length of query: 318 Effective length of database: 348 Effective search space: 110664 Effective search space used: 110664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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