Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 5210054 Shew_2501 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__PV4:5210054 Length = 337 Score = 212 bits (539), Expect = 1e-59 Identities = 112/323 (34%), Positives = 195/323 (60%), Gaps = 9/323 (2%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL++ NL +E G VKA++ +S LN GE G+VGESGSG+++ ++L + N Sbjct: 1 MPLLDIRNLTIELDTPHGRVKALERVSLTLNPGEVHGLVGESGSGRTLLAKAILGIPGHN 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 I ++ G++L+ ++ E R + G ++++IFQ+P++SL+P I VG Q++E + ++ Sbjct: 61 WTIQADRMMWDGQNLMDMSPSERRVLMGSEMAMIFQDPISSLDPAIAVGTQIIEAMPENK 120 Query: 122 LM----KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLI 177 + + + R++A + L +VGI E+ K +Y ++ S G Q+VMIA+A+A P+LLI Sbjct: 121 ELPWWKRGSDKRKKAQQWLHKVGIKETQKIMSSYAWELSDGECQKVMIAIAVANQPRLLI 180 Query: 178 ADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEA 237 ADEPT +++V QAQI LL +L + +S++ I+H+L + +CDR+ MY+G+++E Sbjct: 181 ADEPTNSMEVRTQAQIFRLLSKLNQLQNVSILLISHELETLSQWCDRLTVMYSGQVMESG 240 Query: 238 PVEEILKTPLHPYTKGLLNSTLEIGS---RGKKLVPIPGNPPNPTKHPSGCKFHPRCSFA 294 +++ P HPYTK LL++ + + + +PG+ P P GC+ PRC A Sbjct: 241 VTSDVIANPYHPYTKALLDNIPDYSNPEHHKTMMQTLPGSAPALQHLPIGCRLGPRCPQA 300 Query: 295 MEICQREEPPLVNISENHRVACH 317 ++C + P + ++ ACH Sbjct: 301 QKLCVNQ--PSLCHQKDRYFACH 321 Lambda K H 0.320 0.139 0.401 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: 270 Number of extensions: 9 Number of successful extensions: 3 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: 324 Length of database: 337 Length adjustment: 28 Effective length of query: 296 Effective length of database: 309 Effective search space: 91464 Effective search space used: 91464 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: 49 (23.5 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