Align Histidine transport system permease protein HisM (characterized)
to candidate AZOBR_RS00680 AZOBR_RS00680 ABC transporter permease
Query= SwissProt::P0A2I7 (235 letters) >FitnessBrowser__azobra:AZOBR_RS00680 Length = 234 Score = 115 bits (288), Expect = 7e-31 Identities = 78/217 (35%), Positives = 120/217 (55%), Gaps = 12/217 (5%) Query: 17 GYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTP-LYVQL 75 G G A+T+ + +S+ V+G + + A ++S N + ++T + RG P L V Sbjct: 14 GQLLGGAAMTVAVSVSAFVLGLVFGSLGASAKLSRNLALTGVAEVYTTVVRGVPELLVIY 73 Query: 76 LVFYSGMYTLEIV------KGTDLLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVP 129 L+F+ G + V +G LNAF + VLA+ L + AY+TE+ GA+++VP Sbjct: 74 LLFFGGSGAVMAVGRVFGYEGYIELNAF-----SIGVLAVGLISGAYSTEVIRGAVQAVP 128 Query: 130 HGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIA 189 HG+IEAARA G S + + R I++P LR ALP N L L TAL + ++++++ Sbjct: 129 HGQIEAARACGMSRWLILRRILVPQTLRYALPGLGNVWQLTLKDTALISVTALAEIMRVS 188 Query: 190 RDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAER 226 +T QPF + AAVLYLL++ V F RAER Sbjct: 189 HVAAGSTRQPFLFYTTAAVLYLLLTTVSTVAFERAER 225 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: 145 Number of extensions: 10 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: 234 Length adjustment: 23 Effective length of query: 212 Effective length of database: 211 Effective search space: 44732 Effective search space used: 44732 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