Align Probable binding protein component of ABC transporter, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate BPHYT_RS14005 BPHYT_RS14005 ABC transporter
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS14005 Length = 292 Score = 290 bits (743), Expect = 2e-83 Identities = 144/292 (49%), Positives = 195/292 (66%), Gaps = 4/292 (1%) Query: 10 TAIVAALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGK-PIGYSHDLQ 68 T AA L+ DELTGTL+KI + G + LG R+ASIPFSY GK +GYS + Sbjct: 4 TTFGAASLACSAQTDELTGTLRKIHDDGVVVLGVREASIPFSYFD---GKGTVGYSQTIA 60 Query: 69 LKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDFSVGI 128 L++VE +KK L +P+LKV VTS R P++ N +D+ECGSTT+ ER+ FS Sbjct: 61 LQIVEEIKKTLGMPQLKVHEITVTSSNRTPMLLNNQIDLECGSTTHTVERENLAAFSNSF 120 Query: 129 FEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKDHGES 188 F+ R++++K A I DF DL GK VVTTAGT+ ERLL+ +N DK + M I SA+DH E+ Sbjct: 121 FQYAVRMIARKNAGITDFQDLAGKAVVTTAGTSDERLLRRLNTDKLLNMRITSARDHSEA 180 Query: 189 FMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFKKVVD 248 F L+ GRAVAF+MD+ ++YG + +PDD+VV GTP +E+Y CM RKGD F+ +V+ Sbjct: 181 FNTLKDGRAVAFVMDEPIVYGFKSTDPRPDDFVVTGTPLGYEVYACMFRKGDEPFRTLVN 240 Query: 249 KAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDKAAE 300 I SGE ++Y +WFTQPIPP G+NLNFP+SE+ + L A P D+A + Sbjct: 241 GVIARGQTSGEAERLYRQWFTQPIPPHGINLNFPLSEQNRALFAHPNDRALD 292 Lambda K H 0.314 0.132 0.370 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: 259 Number of extensions: 11 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: 302 Length of database: 292 Length adjustment: 26 Effective length of query: 276 Effective length of database: 266 Effective search space: 73416 Effective search space used: 73416 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: 42 (22.0 bits) S2: 48 (23.1 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