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 Ac3H11_4825 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4825 Length = 343 Score = 266 bits (679), Expect = 7e-76 Identities = 140/324 (43%), Positives = 199/324 (61%), Gaps = 10/324 (3%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL V+NL++ G AV G+S+ L +GE+LG++GESG GKS++ +SL+ L+ + Sbjct: 1 MSLLEVSNLRIRLQTHRGPADAVRGVSFSLARGETLGLIGESGCGKSITAMSLMGLLPES 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 ++ G F G++L+ ++ +RG I ++FQ PMT+LNP+ +G QV EP+ HR Sbjct: 61 AQVT-GSIRFDGQELVGRTDAQMCQMRGNRIGMVFQEPMTALNPVHTIGRQVAEPLRLHR 119 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 M AR AI LL+RVGIP + +RF YP QFSGG RQR+ IAMALAC P LLIADEP Sbjct: 120 GMNAAAARTEAIALLDRVGIPNAAQRFDAYPHQFSGGQRQRITIAMALACGPDLLIADEP 179 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 TTALDVTIQ QI++L+ +L E M++I I+HDL V + DR++ MY G +VE Sbjct: 180 TTALDVTIQQQILDLISDLVAERNMALILISHDLGVISQNVDRMMVMYGGSVVESGSTAS 239 Query: 242 ILKTPLHPYTKGLLNSTLEIGS-----RGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAME 296 + HPYT+GL + +G+ + +L IPG P P+GC F RCS+ ++ Sbjct: 240 VFSAMTHPYTRGLFAARPHLGTVHAPGQRPRLSTIPGTVPELVDLPAGCPFAGRCSYTID 299 Query: 297 ICQREEPPLVNISE----NHRVAC 316 C +E P ++ +H V C Sbjct: 300 TCHQESPAATLVATDADGDHVVRC 323 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: 256 Number of extensions: 14 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: 343 Length adjustment: 28 Effective length of query: 296 Effective length of database: 315 Effective search space: 93240 Effective search space used: 93240 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