Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate H281DRAFT_05703 H281DRAFT_05703 glycerol 3-phosphate ABC transporter membrane protein /carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__Burk376:H281DRAFT_05703 Length = 294 Score = 127 bits (320), Expect = 2e-34 Identities = 84/281 (29%), Positives = 142/281 (50%), Gaps = 8/281 (2%) Query: 2 RHKEALAGYLFSSPYLAGFLIFFAIPSAMSVYYCFTRGVGSF----EFAGLDNFKSVIAS 57 R +L YL +P LA +FF P+ +++ T+ +F EF GL NF+ + A Sbjct: 6 RFGTSLLPYLLVAPQLAITALFFLWPAGEALWQS-TQSQDAFGTSSEFVGLANFRQLFAD 64 Query: 58 NSYRLAVKNTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILV 117 Y + TLIF ++ +++SLLLA+ ++ RGA+ ++ + P + A ++ Sbjct: 65 PLYLSSFNTTLIFCALVTVSGLVISLLLAVCADRVTRGAKGYQTLLIWPYAVAPAIAAVL 124 Query: 118 WQITFN-EFGVLNNLLNHFGIAGVEWLNSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIP 176 W FN G++ L +GI LN+ ++ ++VL VWK YN + F AGL +IP Sbjct: 125 WSFLFNPSIGLVTFALAKYGIVWNHALNAGQAMFLVVLASVWKQVSYNFLFFYAGLQAIP 184 Query: 177 KDYYDAASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINS-FKVFREAYLLCGNYPPLN 235 + +AA+IDGAG + F I LPLL PT FF+ +I+I + F F G P + Sbjct: 185 RSLIEAAAIDGAGPVRRFFGIALPLLSPTSFFLLVINITYAFFDTFPVIDAATGGGPAQS 244 Query: 236 -MYMLQHFMNNNFNNLNYQRLSTASLLMELFIVAIVFLMYK 275 ++ F L+ S+++ + +VA+ + ++ Sbjct: 245 TRTLIYKIFAEGFQGLDIGSSGAQSVVLMVIVVALTVVQFR 285 Lambda K H 0.331 0.144 0.444 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: 211 Number of extensions: 14 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: 284 Length of database: 294 Length adjustment: 26 Effective length of query: 258 Effective length of database: 268 Effective search space: 69144 Effective search space used: 69144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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