Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 119 bits (298), Expect = 1e-31 Identities = 75/248 (30%), Positives = 134/248 (54%), Gaps = 15/248 (6%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 ++E+ V K FG ALD V++ + KGE V +LG +G GK+TL+++I+G+ G++ Sbjct: 9 IIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRI 68 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 GK++ P+ + T++Q AL P L +Y NI ++ K ++ + K Sbjct: 69 SGKEITQTPPH---KRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALK 125 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV-LE 182 ++ D V++LSGGQ+Q VA+ARA+ +++L+DEP AAL + + + +E Sbjct: 126 MVGMTDYEYRD----VDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQME 181 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFA- 241 L K G+ + +TH+ + ++D I V+ GKI ++ T ++ E + SF Sbjct: 182 LKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKI----QQIGTPIDIYNEPINSFVA 237 Query: 242 --LGKVNL 247 +G+ N+ Sbjct: 238 DFIGESNI 245 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: 238 Number of extensions: 10 Number of successful extensions: 4 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: 251 Length of database: 463 Length adjustment: 28 Effective length of query: 223 Effective length of database: 435 Effective search space: 97005 Effective search space used: 97005 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