Align Histidine transport system permease protein HisM (characterized)
to candidate Pf6N2E2_2959 Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
Query= SwissProt::P0A2I7 (235 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2959 Length = 242 Score = 118 bits (295), Expect = 1e-31 Identities = 77/210 (36%), Positives = 115/210 (54%), Gaps = 5/210 (2%) Query: 22 GVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTP-LYVQLLVFYS 80 G +T+ L S+++ LL ++ A ++SS K +R P L+T + RG P L + LL+FYS Sbjct: 26 GTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLLIFYS 85 Query: 81 GMYTLEIVKGTDLLNAFFRS--GLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARA 138 L + TD + + V+ L AY TE F GAI SVP G++EAA A Sbjct: 86 LQTWLTSL--TDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAATA 143 Query: 139 YGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINSATYQ 198 YG + +R ++ P +R ALP N ++ML +TAL + DL+K A+D +TYQ Sbjct: 144 YGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKSTYQ 203 Query: 199 PFTAFGIAAVLYLLISYVLISLFRRAERRW 228 F +AA++YLLI+ + R ERR+ Sbjct: 204 LFYFLVLAALIYLLITSASNFILRWLERRY 233 Lambda K H 0.330 0.141 0.429 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: 146 Number of extensions: 9 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: 235 Length of database: 242 Length adjustment: 23 Effective length of query: 212 Effective length of database: 219 Effective search space: 46428 Effective search space used: 46428 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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