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 H281DRAFT_03129 H281DRAFT_03129 oligopeptide transport system substrate-binding protein
Query= TCDB::Q9X268 (642 letters) >FitnessBrowser__Burk376:H281DRAFT_03129 Length = 538 Score = 161 bits (408), Expect = 6e-44 Identities = 107/345 (31%), Positives = 174/345 (50%), Gaps = 18/345 (5%) Query: 68 VVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEFAWKRAASPETPTLPLWASP 127 VVP V +S+T + T+ F LR D RWSNG PVTA DF +AW+R P+T + + Sbjct: 80 VVPGVAQSWTRTGPD-TWVFKLRHDARWSNGQPVTAADFIYAWQRVLDPKTGSK--YTVL 136 Query: 128 VQYIKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSFINMLVLGGAMPLHRKTVQE 187 V+++KN +G PL LG +A+D YT++VT P F + + P++R V Sbjct: 137 VEFVKNAKAILAGKAPLASLGARAVDPYTIEVTTEVPAAFFPQLAAMPTMAPVNRDVVAR 196 Query: 188 HPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFPGNVDRIV---LKAGGLGLQ 244 +W +P FVGNGPY++ + PN +V ++K Y + ++ ++ ++ Sbjct: 197 FGNEWTRPGNFVGNGPYMLADWQPNNRLVGAKSKTYWNASKVVITKVTYLPIENDETAMR 256 Query: 245 QYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVGYEIT-RSLSPVFDDIRIRK 303 Y AG+ D + G ++A +KQ EL ++G+Q Y + + P+F D R+R+ Sbjct: 257 MYQAGQFDYTYSIPSG--IYAQVSKQFGPEL--KTGLQIATYYYSLNNEDPIFKDKRVRQ 312 Query: 304 ALAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIAEAVK----GIPYDP--EQAKKLLAEA 357 AL+M +D+ +LT + +P + S ++ A K G P + A+ LL A Sbjct: 313 ALSMVLDRDLLTQRLTADGELPMYGLISKGTQGAAVFKPDWAGWPMAKRVDYARNLLKSA 372 Query: 358 GYPNGKGFPKVKFYITG-ASDPVAEALVDQWKKVLGITFEIENIE 401 GY + K Y T VA +W+ LG+ ++EN+E Sbjct: 373 GYSDAKPLTFTLTYNTNDLHKKVALFATSEWRTKLGVNTKLENVE 417 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: 928 Number of extensions: 50 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: 1 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