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 8501089 DvMF_1825 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Miya:8501089 Length = 339 Score = 208 bits (529), Expect = 2e-58 Identities = 109/303 (35%), Positives = 179/303 (59%), Gaps = 8/303 (2%) Query: 16 RVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKD 75 R +V AV+ +S+ + GE+L +VGESG GKS +++ L G GE ++ G+ Sbjct: 37 RKRTVVHAVNDVSFDILPGETLSVVGESGCGKSTLARTVIGLYRATG----GEILYRGER 92 Query: 76 LLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL-MKNEEARERAIE 134 + L+ + R + + ++FQ+P SLNP ++V + EP+ +H + + + R R + Sbjct: 93 IDNLSDNGMLPYRTR-MQMVFQDPYASLNPRMKVREILEEPVRFHNPGISDADVRARVAD 151 Query: 135 LLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIM 194 ++E+VG+ +P + YP +FSGG RQR+ IA AL P+ ++ADEP +ALDV+IQAQ++ Sbjct: 152 VMEQVGV--NPLWGVRYPHEFSGGQRQRISIARALVVDPEFIVADEPISALDVSIQAQVL 209 Query: 195 ELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGL 254 L+ +++E+ ++ +FI+HDLSV + R+ MY G + E A E++ P HPYT+ L Sbjct: 210 NLMMDMQEKRNLTYLFISHDLSVVEHISTRVAVMYLGSLCELASAEDLFGNPRHPYTRAL 269 Query: 255 LNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNISENHRV 314 L++ IG + + + G+ P P P+GC FH RC A C +E P + +V Sbjct: 270 LSAIPRIGGKAAGHIKLSGDVPTPINLPTGCVFHGRCQHANARCMQEVPKARQLEGGAQV 329 Query: 315 ACH 317 ACH Sbjct: 330 ACH 332 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: 281 Number of extensions: 13 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: 324 Length of database: 339 Length adjustment: 28 Effective length of query: 296 Effective length of database: 311 Effective search space: 92056 Effective search space used: 92056 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