Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 255 bits (652), Expect = 2e-72 Identities = 169/475 (35%), Positives = 254/475 (53%), Gaps = 13/475 (2%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 + K F AL+++S PG+ HAL+G NGAGKSTL+ IL G P +G ++ Sbjct: 21 IGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTMD 80 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK 139 + D+ VA ++Q ++ +++VAENLF+ P G+I+ +R+ A A L Sbjct: 81 FKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGLA 140 Query: 140 IDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQRE 199 ++ + G LS+ RQLVEIA+ALS GA I DEPT+ L EI RL I L+ E Sbjct: 141 DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDE 200 Query: 200 GVTFLFISHHLQEVYEICQAVTVLRDARHI-VSAPVSALPREQLIEAMTGERGGLAVADA 258 G L++SH ++EV+ IC AVTV +D R++ +S L +QL+ M G R + D Sbjct: 201 GKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVG-RDIQDIYDY 259 Query: 259 AARGALPADTAVALELKELTGADY-EGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317 R AVAL++ L G E VSF V +GE++GL G +GRT + ++GL Sbjct: 260 RPR----QRGAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSGLAR 315 Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377 G + + G L ++A GI P+DR EG++ SVAEN +++ FG Sbjct: 316 HSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFG 375 Query: 378 IAAPA---KKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLID 434 K NA ++ I AL + + LSGGNQQK ++ R L+ VL+L + Sbjct: 376 CLLRGLWEKDNA--EQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDE 433 Query: 435 PTAGVDVKSKEALLSVVDRVREEGKAVLVVSGEL-DDLRTCDRVLVMFRGRVAAE 488 PT G+D+ +K + ++ + EG AV+VVS +L + + DR+LV+ G + E Sbjct: 434 PTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGE 488 Lambda K H 0.318 0.134 0.377 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: 569 Number of extensions: 41 Number of successful extensions: 7 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: 510 Length of database: 514 Length adjustment: 35 Effective length of query: 475 Effective length of database: 479 Effective search space: 227525 Effective search space used: 227525 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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