Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 153 bits (387), Expect = 4e-42 Identities = 92/222 (41%), Positives = 130/222 (58%), Gaps = 14/222 (6%) Query: 3 SVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATS 62 +++I++V + F R AL VD E+ D + + +LGPSG GK+TLLR +AGL+ + Sbjct: 2 TIAIRSVEKQFG-----RYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDA 56 Query: 63 GRVLLDGAPVEGPGAER---GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQK----ER 115 G+VL DG V A G VFQ Y LF +T+ +NI FGL R + K R Sbjct: 57 GQVLFDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARR 116 Query: 116 AAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQ 175 + V L G +P QLSGG +QR A++RALA P +LL+DEPFGALD R ++ Sbjct: 117 VEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLR 176 Query: 176 ELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIK 217 L + +A T +FVTHD +EA+ +A+RVA+ + GRI+ Sbjct: 177 RELRRVHDATGVTTIFVTHDQEEALELADRVAILN--NGRIE 216 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: 194 Number of extensions: 5 Number of successful extensions: 3 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: 339 Length adjustment: 26 Effective length of query: 233 Effective length of database: 313 Effective search space: 72929 Effective search space used: 72929 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 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