Align LacK, component of Lactose porter (characterized)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 351 bits (901), Expect = e-101 Identities = 201/372 (54%), Positives = 248/372 (66%), Gaps = 15/372 (4%) Query: 1 MAEVRLTDIRKSYGS-LEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGE 59 MA + L ++K+YG VI+ V+LE+ EF VF+GPSGCGKSTLLRMIAGLED++ G+ Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 LTIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAK 119 L IGG VMNDV ++RG+AMVFQ+YAL+PHMTV ENM F L+ A KDEI+R+V AA+ Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120 Query: 120 ILELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARL 179 IL+L+AL++R+PKALSGGQRQRVAIGRAIVRQP VFLFDEPLSNLDA LR R+EIARL Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HKEL-NATIVYVTHDQVEAMTLADKIVVM-------RGGIVEQVGAPLALYDDPDNMFVA 231 HK+ A++VYVTHDQ+EAMTLADKIV++ R G + Q+GAPL LY P + FVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240 Query: 232 GFIGSPRMNFLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHF- 290 GFIGSPRMNFLP I + V V L + A Q AVT+GVRPEH Sbjct: 241 GFIGSPRMNFLPG-RIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLE 299 Query: 291 ---LPAGSGDTQLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGI 347 L + D L+ V +VE LG SYV+ PG +I + GD + + Sbjct: 300 FADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQ-PGGVALIAKAPGDTRLAPGDRANLRV 358 Query: 348 SAKTSFLFDASG 359 + LF G Sbjct: 359 PRHATHLFTEDG 370 Lambda K H 0.320 0.137 0.390 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: 407 Number of extensions: 17 Number of successful extensions: 4 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: 363 Length of database: 383 Length adjustment: 30 Effective length of query: 333 Effective length of database: 353 Effective search space: 117549 Effective search space used: 117549 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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