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 AZOBR_RS23930 AZOBR_RS23930 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__azobra:AZOBR_RS23930 Length = 329 Score = 275 bits (703), Expect = 1e-78 Identities = 145/316 (45%), Positives = 198/316 (62%), Gaps = 4/316 (1%) Query: 5 LNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 L + +L F +G V +DG+S + G +L +VGESGSGKS++ LS L L+ GR+ Sbjct: 1 LELRDLTTVFPGDDGPVTVIDGVSLAVRAGGTLAVVGESGSGKSMTFLSALGLVAAPGRV 60 Query: 65 VDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMK 124 GE G D+L E LR +RG IS+IFQ+P+T+LNP+ +G Q++E + H+ + Sbjct: 61 RRGEVRIDGADILHQPPERLRRLRGAVISMIFQDPLTALNPVFTIGEQIVEVLRAHQRIG 120 Query: 125 NEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTA 184 AR RAIELL RV IP+ +R +YP Q SGG RQRV+IAMA+A PK+LIADEPTTA Sbjct: 121 RTAARARAIELLARVQIPDPARRVDDYPHQLSGGQRQRVLIAMAIALSPKILIADEPTTA 180 Query: 185 LDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILK 244 LDVT+QAQI++LL +L+ E GM+++ ITHDL + + D + MYAG++VE +EE+ Sbjct: 181 LDVTVQAQILDLLADLQAETGMALVLITHDLGLVAKYADDVAVMYAGRLVETGSMEEVFT 240 Query: 245 TPLHPYTKGLLNSTLEI-GSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFA---MEICQR 300 P HPYT+ L S + G ++L I G PPN + P GC F PRC+ + C R Sbjct: 241 RPRHPYTRALFRSIPRLDGPVDEELPAIEGQPPNVARLPPGCAFEPRCTVGRGRADCCTR 300 Query: 301 EEPPLVNISENHRVAC 316 PL HR AC Sbjct: 301 RPLPLAGDRSGHRSAC 316 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: 280 Number of extensions: 11 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: 329 Length adjustment: 28 Effective length of query: 296 Effective length of database: 301 Effective search space: 89096 Effective search space used: 89096 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: 48 (23.1 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