Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 158 bits (399), Expect = 2e-43 Identities = 89/211 (42%), Positives = 130/211 (61%), Gaps = 8/211 (3%) Query: 3 SVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATS 62 ++ I+ + + FE AL+ +D VR + + LGPSGCGK+TLLRI+AGL+ TS Sbjct: 19 ALEIKGIHKNFENFS-----ALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTS 73 Query: 63 GRVLLDGAPVEG-PGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYF 119 G ++ G + P +ER G+VFQSY LFP LTI +N+ +GL M +A+ + R A Sbjct: 74 GSIVQSGRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAEL 133 Query: 120 IAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLL 179 +A GL +P QLSGG QQR A+ARALA +P +LL+DEP ALD RV ++ + Sbjct: 134 LAMAGLPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIR 193 Query: 180 GIWEAERKTVLFVTHDIDEAIFMANRVAVFS 210 + + T + VTHD +EA+ M++R+ V + Sbjct: 194 RLQKQVGITTIMVTHDQEEALSMSDRIVVMN 224 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: 195 Number of extensions: 5 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: 377 Length adjustment: 27 Effective length of query: 232 Effective length of database: 350 Effective search space: 81200 Effective search space used: 81200 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 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