Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate 3606891 Dshi_0321 ABC transporter related (RefSeq)
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Dino:3606891 Length = 258 Score = 224 bits (572), Expect = 1e-63 Identities = 121/263 (46%), Positives = 173/263 (65%), Gaps = 12/263 (4%) Query: 14 DEPVAQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCIN 73 D+ A V+ + ++++ ++K YG+ VL+ ++L +G+ I + G SGSGKST++RCIN Sbjct: 5 DQAPAMTVSDEVAIEIDKMNKWYGQFHVLRDINLTVYRGERIVICGPSGSGKSTLIRCIN 64 Query: 74 FLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENI 133 LE+ AG IT+DG + + + +R+ + M FQHFNL+ H+T+LEN Sbjct: 65 ALEEHQAGSITVDGTLL----------SSDLKNIDTIRSEVGMCFQHFNLFPHLTILENC 114 Query: 134 TMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEI 193 T+AP V EAE A +L+KV +P + A++YP LSGGQQQRVAIAR+L M P I Sbjct: 115 TLAPIWVRKTPKKEAEATAMHFLEKVKIPDQ-ANKYPGQLSGGQQQRVAIARSLCMRPRI 173 Query: 194 ILFDEPTSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGR-VEE 252 +LFDEPTSALDPE++ EVL + LAEEG TM+ VTHEMGFARQV+++V+F+ G+ VE+ Sbjct: 174 MLFDEPTSALDPEMIKEVLDTMIELAEEGMTMICVTHEMGFARQVANRVIFMDAGQIVEQ 233 Query: 253 HGDARILDQPNSERLQQFLSNRL 275 + P S+R + FLS L Sbjct: 234 NEPEEFFGNPQSDRTKLFLSQIL 256 Lambda K H 0.319 0.133 0.372 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: 189 Number of extensions: 8 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: 276 Length of database: 258 Length adjustment: 25 Effective length of query: 251 Effective length of database: 233 Effective search space: 58483 Effective search space used: 58483 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: 47 (22.7 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