Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3607445 Dshi_0858 ABC transporter related (RefSeq)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Dino:3607445 Length = 230 Score = 166 bits (421), Expect = 3e-46 Identities = 94/218 (43%), Positives = 133/218 (61%), Gaps = 5/218 (2%) Query: 10 PLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVV 69 PL+Q+ GV YG +AL GVD+ + +G ++L+G NG GKST + T+CG G V Sbjct: 3 PLVQIEGVTAAYGASQALFGVDLTLKEGGALALMGRNGMGKSTTLKTLCGLLPPTGGRVR 62 Query: 70 FEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTL 129 G +IT P H IARL + PEGRR F +TV ENL A + D+ ++ L Sbjct: 63 LAGVEITGRPAHRIARLGVGLVPEGRRCFAPLTVAENLLAAA-----RPGPWDMARVGAL 117 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FPRL ER Q +LSGGEQQML+IGRALM P+LL+LDE + GLAP++ + I+ AI +L Sbjct: 118 FPRLAERRDQVARSLSGGEQQMLAIGRALMTNPRLLVLDEATEGLAPVVRQEIWAAIARL 177 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGS 227 GL++ LV+++ +++ A ++ G+ SGS Sbjct: 178 RAEGGLSLILVDKSLRELRQVADTAVILARGRTVWSGS 215 Lambda K H 0.320 0.137 0.387 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: 185 Number of extensions: 7 Number of successful extensions: 2 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: 247 Length of database: 230 Length adjustment: 23 Effective length of query: 224 Effective length of database: 207 Effective search space: 46368 Effective search space used: 46368 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: 46 (22.3 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