Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 123 bits (309), Expect = 7e-33 Identities = 71/227 (31%), Positives = 129/227 (56%), Gaps = 6/227 (2%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 ++ ++ + + KSFG V+A ++++I G + ALLG+NGAGKSTL+ I+SG D G Sbjct: 31 VTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGI 90 Query: 61 LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120 + +G+ V F SP DA GI +YQ L+ + + N+ L + + +L+ M Sbjct: 91 IHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ---SGAWLSPVHMSRV 147 Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180 +L + I D +V +LS G+RQ V + + +Y ++++++DEPTA L+ E ++ Sbjct: 148 VAELAARYGLDI-DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQL 206 Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII--FHKKK 225 E + + G ++ I+H + + +AD I +L RG+++ FH+ + Sbjct: 207 FEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESE 253 Score = 77.0 bits (188), Expect = 7e-19 Identities = 61/228 (26%), Positives = 104/228 (45%), Gaps = 8/228 (3%) Query: 8 RDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEG-- 65 R +H A L G+S E+ KGEV A+ G G G+ L++ ++G +P G++ G Sbjct: 283 RVLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIP 342 Query: 66 -KKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLARE--VTNKIFLNKKKMMEESK 122 ++ +P I Q LA L + N L T FL++K ++ Sbjct: 343 WRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAAR 402 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 +L ++ +LSGG Q + V R Y +I+ + PT L + +V Sbjct: 403 DILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEV-- 460 Query: 183 LARNLK-KKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETN 229 AR L+ + GVL+++ ++ + +ADR+ V+ RG I + +TN Sbjct: 461 WARLLEVRSHAGVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTN 508 Lambda K H 0.318 0.137 0.371 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: 246 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 524 Length adjustment: 29 Effective length of query: 222 Effective length of database: 495 Effective search space: 109890 Effective search space used: 109890 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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