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 Pf6N2E2_3406 putative ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3406 Length = 262 Score = 240 bits (612), Expect = 3e-68 Identities = 131/256 (51%), Positives = 176/256 (68%), Gaps = 3/256 (1%) Query: 17 VAQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLE 76 ++ P AA+ L+V +HK YG+ EVLKG+SL + G+ +SLIG SGSGKST LRCIN+LE Sbjct: 1 MSSPSDAAL-LRVHELHKNYGDLEVLKGISLELKPGETLSLIGPSGSGKSTCLRCINYLE 59 Query: 77 QPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMA 136 +P +G I L I R+ +R ++ R +AMVFQ F LW H+ V +N+ + Sbjct: 60 KPTSGEIWLGNELIGQRRDGQRSRLMSDREMAPQRREIAMVFQLFYLWPHLNVRDNVALG 119 Query: 137 PRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILF 196 P + + +A + A L+KV L + A+ YP LSGGQQQRVAIARALA +P++ILF Sbjct: 120 PIKAQGMPRKQAYELADAMLEKVHLRHK-AESYPEQLSGGQQQRVAIARALAQQPKVILF 178 Query: 197 DEPTSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDA 256 DEPTSALDPELVGEVL VI+ LAEEGR+M+MVTHE+ FAR V+ +V+F+ GR+ E G + Sbjct: 179 DEPTSALDPELVGEVLAVIRELAEEGRSMIMVTHEVRFARDVADRVIFMDGGRIVEQGPS 238 Query: 257 R-ILDQPNSERLQQFL 271 R ++D P ER + FL Sbjct: 239 RQVIDNPCHERTRSFL 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: 229 Number of extensions: 9 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: 262 Length adjustment: 25 Effective length of query: 251 Effective length of database: 237 Effective search space: 59487 Effective search space used: 59487 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