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 CA265_RS04175 CA265_RS04175 phosphonate ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Pedo557:CA265_RS04175 Length = 232 Score = 112 bits (280), Expect = 9e-30 Identities = 77/233 (33%), Positives = 130/233 (55%), Gaps = 12/233 (5%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 ++ + NL+ + E A++GI+ + GE + I+G SG GKS +LL ++ + Sbjct: 1 MIKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKS----TLLNVMGLLDK 56 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 +G F+ +LL LN E N R +++ +FQN +L + V + P+I++++ Sbjct: 57 PENGSYKFIDTELLTLNDRERSNFRKRNMGFVFQN--FNLIDELTVFENIELPLIYNKIP 114 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 E ++ E++ER+ I R ++P Q SGG +QRV +A AL PKL++ADEPT Sbjct: 115 AGER-KKLVNEIIERMNIVN---RSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTG 170 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 LD + ++MELL EL E G +++ +TH S +F +RII + G ++ E Sbjct: 171 NLDSSHGNEVMELLCELNET-GTTIVMVTHS-SHDASFSNRIINLKDGHVISE 221 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: 160 Number of extensions: 8 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: 232 Length adjustment: 25 Effective length of query: 299 Effective length of database: 207 Effective search space: 61893 Effective search space used: 61893 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: 47 (22.7 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