Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_013402865.1 CALHY_RS04750 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000166355.1:WP_013402865.1 Length = 370 Score = 138 bits (348), Expect = 1e-37 Identities = 76/211 (36%), Positives = 120/211 (56%), Gaps = 7/211 (3%) Query: 1 MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60 M+SV ++ V + + A+ + ++ D +F+ ++GPSGCGK+T LR++AGL+ Sbjct: 1 MASVRLKGVYKRYPGG----VTAVSDFNLDIEDKEFIVLVGPSGCGKTTTLRMIAGLEEV 56 Query: 61 TSGRVLLDGAPVEG-PGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAA 117 T G + + V P +R MVFQ+Y L+P +T+ +N+ FGL+ R P+ + K R Sbjct: 57 TEGEIYIGDKLVNDVPPKDRDIAMVFQNYALYPHMTVFENMAFGLKLRKFPKDEIKRRVH 116 Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177 +G+ PK LSGG +QR A+ RA+ +PK+ LMDEP LD + RV M+ Sbjct: 117 EAAKILGIEHLLDRKPKALSGGQRQRVALGRAIVREPKVFLMDEPLSNLDAKLRVQMRTE 176 Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAV 208 L + + T ++VTHD EA+ M R+ V Sbjct: 177 LSKLHKRLGTTFIYVTHDQTEAMTMGTRIVV 207 Lambda K H 0.322 0.136 0.394 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: 208 Number of extensions: 8 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: 259 Length of database: 370 Length adjustment: 27 Effective length of query: 232 Effective length of database: 343 Effective search space: 79576 Effective search space used: 79576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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