Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__PV4:5210167 Length = 265 Score = 124 bits (310), Expect = 2e-33 Identities = 81/251 (32%), Positives = 139/251 (55%), Gaps = 17/251 (6%) Query: 2 SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61 ++L V+ +S+ +G ++A+ DVSFEV G V S+IG NGAGKT++L ++SG RP G I Sbjct: 4 TILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGTIH 63 Query: 62 FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGA-FLKKN------------ 108 F Q++ + G+ + + +F ++V++N+ +G L KN Sbjct: 64 FDNQDVTHLRPNARADLGIGRTFQNLALFGHMSVLDNIMVGRHHLMKNNWLTGPLYWASP 123 Query: 109 -REENQANLKKV--FSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSM 165 ++E A+ ++V F + + A TLS G ++ + + RA+ PKL+LLDEP Sbjct: 124 AQKEELAHRRQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELARAMALNPKLILLDEPMA 183 Query: 166 GLAPIFIQEIFDIIQDIQKQ-GTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELA 224 G+ +++ I D+ ++ G TV++IE + + IS VL+ GK ++SG + + Sbjct: 184 GMNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMVLDFGKKLISGLPEAVM 243 Query: 225 SSEEVRKAYLG 235 + E VR+AYLG Sbjct: 244 ADEHVRQAYLG 254 Lambda K H 0.315 0.134 0.358 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: 154 Number of extensions: 6 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: 236 Length of database: 265 Length adjustment: 24 Effective length of query: 212 Effective length of database: 241 Effective search space: 51092 Effective search space used: 51092 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: 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