Align TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BPHYT_RS22050 BPHYT_RS22050 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9X268 (642 letters) >FitnessBrowser__BFirm:BPHYT_RS22050 Length = 538 Score = 160 bits (405), Expect = 1e-43 Identities = 107/349 (30%), Positives = 174/349 (49%), Gaps = 26/349 (7%) Query: 68 VVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEFAWKRAASPETPTLPLWASP 127 +VP V ES++ S T+ F LR D RWSNG PVTA DF ++W+R P+T + + Sbjct: 80 IVPGVAESWSRSGPN-TWVFKLRHDARWSNGQPVTASDFVYSWQRVLDPKTGSK--YTVL 136 Query: 128 VQYIKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSFINMLVLGGAMPLHRKTVQE 187 V+++KN +G PL LGV+A+D YTL+VT P F + + P++R V + Sbjct: 137 VEFVKNAKAILAGKAPLSSLGVRAVDPYTLEVTTEVPATFFPQLTAMATMTPVNRAVVTK 196 Query: 188 HPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFPGNVDRIV---LKAGGLGLQ 244 DW +P FVGNGPY + + P+ +V ++ Y + + ++ ++ ++ Sbjct: 197 FDGDWTRPGNFVGNGPYALTDWQPSNRLVATKSPTYWNNGKVVITKVTYLPIENDETAMR 256 Query: 245 QYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVGYEIT-RSLSPVFDDIRIRK 303 Y AG+ D + G V++ +KQ EL ++G+Q Y + + P F D R+R+ Sbjct: 257 MYQAGQFDYTYSIPSG--VYSQVSKQFGPEL--KTGLQIATYYYSLNNDDPAFKDKRVRQ 312 Query: 304 ALAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIA----------EAVKGIPYDPEQAKKL 353 ALAM +D+ +LT + +P + + +E + K + Y A+ L Sbjct: 313 ALAMVLDRDLLTKRLTADGEVPMYGLIAKGTEGSGVFTPEWANWPMAKRVDY----ARNL 368 Query: 354 LAEAGYPNGKGFPKVKFYITG-ASDPVAEALVDQWKKVLGITFEIENIE 401 L AGY + K Y T VA +W+ LG+T ++EN+E Sbjct: 369 LKTAGYSDAKPLTFTLTYNTNDLHKKVALFATSEWRTKLGVTAKLENVE 417 Score = 26.9 bits (58), Expect = 0.002 Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 3/33 (9%) Query: 416 WAEPGVCTIGGP---VNWQDSGSLMQTADHTFW 445 W PG GP +WQ S L+ T T+W Sbjct: 201 WTRPGNFVGNGPYALTDWQPSNRLVATKSPTYW 233 Lambda K H 0.319 0.138 0.431 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: 980 Number of extensions: 61 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 642 Length of database: 538 Length adjustment: 37 Effective length of query: 605 Effective length of database: 501 Effective search space: 303105 Effective search space used: 303105 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 (21.7 bits) S2: 53 (25.0 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