Align Histidine transport ATP-binding protein HisP (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 145 bits (367), Expect = 1e-39 Identities = 82/228 (35%), Positives = 141/228 (61%), Gaps = 16/228 (7%) Query: 32 GDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLL 91 G+ + ++G SG GK+T R I L +P+ G II NG+NI + K LR L Sbjct: 346 GETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENITHI----------GKTALRKL 395 Query: 92 RTRLTMVFQ--HFNLWSHMTVLENVMEAPIQVLGLSKHDA--RERALKYLAKVGIDERAQ 147 R + ++FQ + +L +++ ++++E P+QV L ++D+ +++ L+ L KVG+ E Sbjct: 396 RKDIQIIFQDPYASLNPKLSIGQSILE-PLQVHKLYRNDSERKQKVLELLDKVGLKEEHF 454 Query: 148 GKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEE-GKTM 206 +YP SGGQ+QRV IARALA++P ++ DE SALD + +VL +++ L E G T Sbjct: 455 NRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLIKDLQSEFGLTY 514 Query: 207 VVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLK 254 + ++H++ +H+S ++ +++GKIEEEG PEQ+F P++ Q+ ++ Sbjct: 515 IFISHDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKAAYTQKLIE 562 Score = 107 bits (267), Expect = 6e-28 Identities = 69/234 (29%), Positives = 129/234 (55%), Gaps = 12/234 (5%) Query: 20 EVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQ 79 + +K +S + + G V+ I+G SGSGKS + + + E A + G+ + +D Sbjct: 21 KAVKQISFKVKKGTVLGIVGESGSGKS--VTSFSIMRLHDERAAKITGE----IDFEDIS 74 Query: 80 LKVADKNQLRLLR-TRLTMVFQH--FNLWSHMTVLENVMEAPIQVLGLSKHDARERALKY 136 L N++R +R +++M+FQ +L T V EA + + + +A++ + Sbjct: 75 LLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIAL 134 Query: 137 LAKVGID--ERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLR 194 +V + E+ YP +SGGQ+QRV IA AL+ +P +L+ DEPT+ALD + +L+ Sbjct: 135 FNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQ 194 Query: 195 IMQQLAEE-GKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSP 247 ++ +L +E M+ ++H++G ++ V +++G+I E+G + +F NPQ P Sbjct: 195 LLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFENPQHP 248 Lambda K H 0.319 0.136 0.383 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: 325 Number of extensions: 13 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: 258 Length of database: 568 Length adjustment: 30 Effective length of query: 228 Effective length of database: 538 Effective search space: 122664 Effective search space used: 122664 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 (21.7 bits) S2: 50 (23.9 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