Align ABC transporter for L-Histidine, periplasmic substrate-binding component 2 (characterized)
to candidate RR42_RS16940 RR42_RS16940 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2562 (321 letters) >FitnessBrowser__Cup4G11:RR42_RS16940 Length = 323 Score = 492 bits (1267), Expect = e-144 Identities = 245/315 (77%), Positives = 276/315 (87%), Gaps = 4/315 (1%) Query: 10 SLAAAAACVMAL---AAPAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGLDVEIKMI 66 SLA A A V+A A AQAQ T++ LGMSGWTGFAPLTLADKAGIFKK+G+DV+IKMI Sbjct: 10 SLAVAVAAVVATLGAAGTAQAQATQVTLGMSGWTGFAPLTLADKAGIFKKHGVDVDIKMI 69 Query: 67 PQKDRHLALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVRGDIKSFAD 126 PQKDRHLALA+ +IQCAATTVETHVAWNANGVPI QI Q+DKSYGADG+AVRGD+K FAD Sbjct: 70 PQKDRHLALAAGAIQCAATTVETHVAWNANGVPITQIVQLDKSYGADGLAVRGDVKGFAD 129 Query: 127 LKGKTIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEP 186 LKGKTIGVDAPGTAPYFGLAWML KNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEP Sbjct: 130 LKGKTIGVDAPGTAPYFGLAWMLKKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEP 189 Query: 187 YLSTVRDNPAAGKILATTLDYPMVMDTVGCDPTWLKANGKAAQALANSYFQALDMIKADP 246 YLS+VR NP GKILATTLDYPMVMDT+GC P WLK N KAAQAL +SYF+ALDMI+ DP Sbjct: 190 YLSSVRQNPDKGKILATTLDYPMVMDTLGCAPKWLKDNPKAAQALVDSYFEALDMIRQDP 249 Query: 247 AKSNEIMGAAVKQTGEQFAKSSSFLRWQDKAANQKFFAGELTTFMKDATAILLEAGIIRK 306 AK+N++MGAAVKQ+GEQFAKSS++LRWQD+ AN+KFF GEL +F K+A +LLE G+IR+ Sbjct: 250 AKANDVMGAAVKQSGEQFAKSSAYLRWQDRDANRKFFGGELASFSKEAAQVLLEIGVIRQ 309 Query: 307 ANEDLAVTFDASFIK 321 D+ +DA FIK Sbjct: 310 V-PDVTALYDARFIK 323 Lambda K H 0.317 0.129 0.374 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: 425 Number of extensions: 8 Number of successful extensions: 1 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: 321 Length of database: 323 Length adjustment: 28 Effective length of query: 293 Effective length of database: 295 Effective search space: 86435 Effective search space used: 86435 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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