Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate Pf1N1B4_4398 Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
Query= uniprot:A0A1N7U128 (237 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4398 Length = 232 Score = 192 bits (489), Expect = 4e-54 Identities = 98/216 (45%), Positives = 142/216 (65%), Gaps = 1/216 (0%) Query: 21 SGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICYT 80 +G +TL + IS+ LG L+IPLAL RVS + +P +YTY+ RGTP+ +QL + Y Sbjct: 17 NGALLTLKVLFISLALGLVLAIPLALMRVSRSPLINFPAWLYTYVIRGTPMLVQLFLIYY 76 Query: 81 GLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAARAYG 140 GL E V+ + L + +A C LAF +NT AY+ E+ AG++++ PHGEIEAA+A G Sbjct: 77 GLAQFEAVRQSVLW-PYLSSATFCACLAFAINTSAYSAELLAGSLKSTPHGEIEAAKAMG 135 Query: 141 LHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETFLTF 200 + L +++P+ALRRALP YSNE+++ML TSLA T+ DI AR ++ +L F Sbjct: 136 MSRLTLYRRILMPSALRRALPQYSNEVLMMLQTTSLASIVTLVDITGAARTVSSRFYLPF 195 Query: 201 QAFGIAALLYMLLSFALVGLFRLAERRWMRFLVPTR 236 +AF A L+Y+ L+F LV LF+LAER W+ +L P + Sbjct: 196 EAFITAGLIYLALTFILVRLFKLAERHWLAYLAPRK 231 Lambda K H 0.332 0.143 0.443 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: 179 Number of extensions: 8 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: 237 Length of database: 232 Length adjustment: 23 Effective length of query: 214 Effective length of database: 209 Effective search space: 44726 Effective search space used: 44726 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 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