Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS29525 BPHYT_RS29525 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__BFirm:BPHYT_RS29525 Length = 260 Score = 248 bits (632), Expect = 1e-70 Identities = 126/259 (48%), Positives = 176/259 (67%), Gaps = 7/259 (2%) Query: 4 LRSLFAALLLPLCAT----AHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAIC 59 ++ L AAL + L AT AHA++W +RFGV YPPFES +DG L GFDI+LGN IC Sbjct: 1 MKKLLAALTVALLATVSIGAHAKDWSTVRFGVDASYPPFESKGSDGKLVGFDIDLGNEIC 60 Query: 60 AKLEVKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRK 119 A+++ KC WV N+FDGMIPAL+A+KFD ++SSM++TP R + I FS++LF +PT ++ +K Sbjct: 61 ARMKAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQIAFSNKLFNTPTRLVAKK 120 Query: 120 SADFGDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDAT 179 + T +SL GK VGV QG++QE YA+ + G ++ YQ+QDQ YADL +GRLDA Sbjct: 121 GSGILPTADSLKGKTVGVEQGTIQETYAKTYWEPKGTKVVPYQNQDQVYADLLSGRLDAA 180 Query: 180 LTDKLEAQLNFLSKPEGSDFK-TGPAFKDP-TLPLDIAMGLRKNDQALRALINKGIAAVQ 237 L D ++A++ FL P G+ F G DP L +G+RK D L+A ++K IA + Sbjct: 181 LQDAVQAEIGFLKTPRGAGFDFVGKNLDDPKILGNGAGIGMRKEDTDLKAKVDKAIADII 240 Query: 238 ADGTYAQIQKKYFGDQDIY 256 DGTY +++KKYF D D+Y Sbjct: 241 KDGTYKKLEKKYF-DFDVY 258 Lambda K H 0.319 0.135 0.393 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: 206 Number of extensions: 4 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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 (21.8 bits) S2: 47 (22.7 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