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 15363 b1243 oligopeptide transporter subunit (NCBI)
Query= TCDB::Q9X268 (642 letters) >FitnessBrowser__Keio:15363 Length = 543 Score = 172 bits (435), Expect = 5e-47 Identities = 115/365 (31%), Positives = 190/365 (52%), Gaps = 17/365 (4%) Query: 70 PAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEFAWKRAASPETPTLPLWASPVQ 129 P V ES+ ++D +TF+LRKD +WS+G PVTA DF ++W+R+ P T + +AS +Q Sbjct: 84 PGVAESWD-NKDAKVWTFHLRKDAKWSDGTPVTAQDFVYSWQRSVDPNTASP--YASYLQ 140 Query: 130 Y--IKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSFINMLVLGGAMPLHRKTVQE 187 Y I + + G KP+ +LGVKA+DD+TL+VTLS P+P F +LV P+ + +++ Sbjct: 141 YGHIAGIDEILEGKKPITDLGVKAIDDHTLEVTLSEPVPYFYKLLVHPSTSPVPKAAIEK 200 Query: 188 HPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFPGNVDRIV---LKAGGLGLQ 244 E W +P V NG Y ++ + N IVL R+ Y + ++++ + + + Sbjct: 201 FGEKWTQPGNIVTNGAYTLKDWVVNERIVLERSPTYWNNAKTVINQVTYLPIASEVTDVN 260 Query: 245 QYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVGYEITRSLSPVFDDIRIRKA 304 +Y +GEID + ++ +F K++ E+H + + YEI P F+D+R+R A Sbjct: 261 RYRSGEID-MTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQ-KPPFNDVRVRTA 318 Query: 305 LAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIAEAVKGIPYD------PEQAKKLLAEAG 358 L + +D+ ++ + V +P + Y P ++ A+ + + E+AKKLLAEAG Sbjct: 319 LKLGMDRDIIVNKVKAQGNMPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAG 378 Query: 359 YPNGKGFPKVKFYITG-ASDPVAEALVDQWKKVLGITFEIENIESGQFSTLQWSDFVPWA 417 Y K Y T +A A WKK +G+ ++ N E F + A Sbjct: 379 YTADKPLTINLLYNTSDLHKKLAIAASSLWKKNIGVNVKLVNQEWKTFLDTRHQGTFDVA 438 Query: 418 EPGVC 422 G C Sbjct: 439 RAGWC 443 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: 1003 Number of extensions: 45 Number of successful extensions: 4 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: 642 Length of database: 543 Length adjustment: 37 Effective length of query: 605 Effective length of database: 506 Effective search space: 306130 Effective search space used: 306130 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