Align ABC transporter related (characterized, see rationale)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Dino:3608728 Length = 376 Score = 134 bits (336), Expect = 4e-36 Identities = 85/257 (33%), Positives = 141/257 (54%), Gaps = 17/257 (6%) Query: 1 MNATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETP 60 M+ ++ + N+ K FG +K + +G+ ++I+G+SG GK+T LR L LE P Sbjct: 7 MDQSSEPIVKFDNVVKRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDP 66 Query: 61 DDGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGP 120 +G++ L GE++ K D MV+Q+ L+ +TV EN +E Sbjct: 67 TEGAIYLDGEQVNGKATWD---------------RDTPMVWQSLALFPFLTVQEN-VEFA 110 Query: 121 MRVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDE 180 ++++ + E + A+ L K+ + E LSGGQ+QRVA+ARAL PK++L DE Sbjct: 111 LKMRGIGKEERRQRADKWLDKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDE 170 Query: 181 PTSALDPELVGEVLRVMRSLAEE-GRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPD 239 P SALD L + V+ +L ++ G T + VTH M A +++RV+ + +GQ+E GTP+ Sbjct: 171 PLSALDAHLKVRMQSVLSNLQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPE 230 Query: 240 EVFVECKSDRFRQFVSS 256 E++ E + +F+ S Sbjct: 231 EIYREPHNRFVAEFLGS 247 Lambda K H 0.318 0.133 0.377 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: 223 Number of extensions: 11 Number of successful extensions: 3 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: 263 Length of database: 376 Length adjustment: 27 Effective length of query: 236 Effective length of database: 349 Effective search space: 82364 Effective search space used: 82364 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 (21.7 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