Align D-cellobiose transporter (MFS superfamily) (characterized)
to candidate N515DRAFT_2416 N515DRAFT_2416 sugar (Glycoside-Pentoside-Hexuronide) transporter
Query= reanno::SB2B:6937231 (444 letters) >FitnessBrowser__Dyella79:N515DRAFT_2416 Length = 466 Score = 290 bits (743), Expect = 5e-83 Identities = 174/445 (39%), Positives = 244/445 (54%), Gaps = 5/445 (1%) Query: 2 LSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPLM 61 L++REK+ YGLGD N+V M FL FFYTD++GIS A VG MFLAVRI DA DP+M Sbjct: 19 LTLREKVGYGLGDAGGNVVIVLAMNFLNFFYTDVYGISPATVGLMFLAVRIFDAFADPVM 78 Query: 62 GYLADRTNTRWGRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAYTA 121 G LAD T +RWGRYRP+ LW A P VLAFT P L + +A TY LL L YTA Sbjct: 79 GILADHTRSRWGRYRPWQLWVALPLGVAVVLAFTVPPLQGDARIAWACVTYLLLSLGYTA 138 Query: 122 INIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVS-ALTLPLVDFFGQGDKAKGYQL 180 IN+PYCA+ A+T + E VS QS+RF ++VS AL + + G G A+GYQ Sbjct: 139 INVPYCAMINAMTVSRREVVSCQSWRFALCGAAALLVSTALPWLVEQWSGAGGPARGYQR 198 Query: 181 TILAMSIVGTVMFLLCFIGTKERDFSSDDNSGNFKAASKALWANDQWRVLSAAAIFLLTG 240 AM V MFL CF+ +ER + + + + + L NDQ +++ + L+T Sbjct: 199 GAAAMCAVAAAMFLCCFLWVRER-VPLRNEAFSLRRLADGLRRNDQLQLMLVMSFLLITI 257 Query: 241 LVLKSTLAIYYVKYFL-GREDMISVFVTSGVVGNIFGVALAKKLADKMCKVKAYIRLQLI 299 L ++ +Y++ Y L G S+F + + I G L L+ + V+ Y + L Sbjct: 258 LNVRGGGYLYFITYVLRGDARYASLFFGAVALAAILGALLVGPLSRWLDTVRFYRYVNLA 317 Query: 300 AAALCMAAWFVP--ADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRTTG 357 AA+ + WF+P AD + L+ + + PL ++ MA DYGQ+KTGVR++G Sbjct: 318 LAAVSASMWFIPGGADAQLAWLLAMFGSGVVLGLCLPLHFSVMAFADDYGQWKTGVRSSG 377 Query: 358 LVYSSVIFFIKLGLAIGGALGGWLLAAYGYQPDVAQTEETRAGILLCFTLYPALASIAVA 417 + ++ + FIKL A G + +L YQ VAQT GI TL PA + +A Sbjct: 378 MNFAFNLVFIKLAWASGAGIIALVLYLVRYQAGVAQTVTALGGITAIQTLIPAAIHLLLA 437 Query: 418 FVMRHYTLDSQRVAEISVSLQQKHS 442 F + LD + +S LQQ+H+ Sbjct: 438 FTLGFCRLDDATMKRVSQDLQQRHT 462 Lambda K H 0.327 0.139 0.421 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: 545 Number of extensions: 29 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: 444 Length of database: 466 Length adjustment: 33 Effective length of query: 411 Effective length of database: 433 Effective search space: 177963 Effective search space used: 177963 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: 51 (24.3 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