Align Histidine transport ATP-binding protein HisP (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 130 bits (327), Expect = 4e-35 Identities = 81/238 (34%), Positives = 130/238 (54%), Gaps = 18/238 (7%) Query: 12 LHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNIN 71 + K++G + L V L+ G++++++G SGSGK+T LR I LE P G ++ +GQ++ Sbjct: 8 VEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVT 67 Query: 72 LVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARE 131 R+ VFQ + L+ HMTV +N+ G K E Sbjct: 68 YAS---------------AAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAE 112 Query: 132 --RALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELV 189 R ++ L K+ E G+YP LSGGQ+QRV+++RALA++P VLL DEP ALD + Sbjct: 113 IARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVR 172 Query: 190 GEVLRIMQQLAE-EGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQS 246 + R ++++ + G T + VTH+ A ++ V L+ G+IE+ G P+QV P++ Sbjct: 173 KSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPET 230 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: 190 Number of extensions: 7 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: 258 Length of database: 339 Length adjustment: 26 Effective length of query: 232 Effective length of database: 313 Effective search space: 72616 Effective search space used: 72616 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: 48 (23.1 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