Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate 3608007 Dshi_1415 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= BRENDA::P68183 (296 letters) >FitnessBrowser__Dino:3608007 Length = 294 Score = 88.2 bits (217), Expect = 2e-22 Identities = 91/307 (29%), Positives = 146/307 (47%), Gaps = 38/307 (12%) Query: 7 KSQKARLFITHLLLLLFIAAIMFPLLMVVAISLR-QGNFATGSLIPEQISWDHWKLALGF 65 +S RLF+ ++LL + A FP L + S + QG+F S + W AL Sbjct: 9 RSMPLRLFLWGVVLLWLMLAA-FPFLWTLWGSFKVQGDF---------FSREDWTNALTG 58 Query: 66 --SVEQADGRITPPPFPVLLWLWNSVKVAGISA----IGIVALSTTCA----YAFARMRF 115 ++ + G T + W+ AG++ + +VA+S T YA +R F Sbjct: 59 VRTLAETGGYFTGGGYAGA-WVQEEFWRAGLNTMIVTLSVVAISLTFGTLGGYALSRSSF 117 Query: 116 PGKATLLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALH-- 173 +L LIF+ P + +LV+ Y L PF LN G + + +A++ Sbjct: 118 KYTFWILMAALIFRAMPHI-TLVSGYLL--------PFFELNIWGILPTTIIVLVAINQP 168 Query: 174 --VWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVP 231 +W ++ +F I L+E+A +DG T +QAFR V++P+ P + + SF+ A + Sbjct: 169 FTLWMLRSFFMNIPKDLDESAMVDGCTRFQAFRRVIIPVMWPGVITTGLFSFLLAYNDFA 228 Query: 232 VASLLLRDVNSYTLAVGMQQYLNPQNYLWG-DFAAAAVMSA-LPITIVFLLAQRWLVNGL 289 V + LL N T+ + +L FA +AV+SA P+ I+ L QR +V+GL Sbjct: 229 VTATLLSQDNQ-TMIPKIASFLGTTQQEGNVMFAVSAVVSATAPLFILVLFFQRQIVSGL 287 Query: 290 TAGGVKG 296 TAG VKG Sbjct: 288 TAGAVKG 294 Lambda K H 0.328 0.141 0.435 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: 298 Number of extensions: 22 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: 296 Length of database: 294 Length adjustment: 26 Effective length of query: 270 Effective length of database: 268 Effective search space: 72360 Effective search space used: 72360 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 (21.8 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