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 GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 225 bits (574), Expect = 7e-64 Identities = 119/250 (47%), Positives = 172/250 (68%), Gaps = 12/250 (4%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 +Q++G+HK +G+ VLK ++L+ RQG+ I L G SGSGKST +RC+N LE+ G I ++ Sbjct: 16 IQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVIN 75 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 G+ + Q++ +R+ + MVFQHFNL+ H+TVL+N T+AP V + Sbjct: 76 GVEL----------TSDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKLPRR 125 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 +AE+ A YL++V +P + A+++P LSGGQQQRVAIARAL M+P+I+LFDEPTSALDPE Sbjct: 126 QAEEIAMHYLERVRIPEQ-ANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPE 184 Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDARI-LDQPNSE 265 +V EVL + +LAE G TML VTHEMGFAR V+ +V+F+ +G + E + + P ++ Sbjct: 185 MVKEVLDTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTNPVND 244 Query: 266 RLQQFLSNRL 275 R + FLS L Sbjct: 245 RTKLFLSQIL 254 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: 201 Number of extensions: 7 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: 255 Length adjustment: 25 Effective length of query: 251 Effective length of database: 230 Effective search space: 57730 Effective search space used: 57730 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