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_695 Oligopeptide transport ATP-binding protein OppD (TC 3.A.1.5.1)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_695 Length = 355 Score = 256 bits (655), Expect = 4e-73 Identities = 145/330 (43%), Positives = 195/330 (59%), Gaps = 18/330 (5%) Query: 5 LNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 L V+ L F G +++V +S+ + GE+L +VGESGSGKSV+ L+L+ L R + Sbjct: 12 LEVSGLSTSFATDAGRIQSVADVSFAIYPGETLALVGESGSGKSVTSLTLMGLHARTSQA 71 Query: 65 -VDGEAIFLGKD-----LLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPII 118 V G+A F+ +D LL + + E R +RG ++++IFQ PMTSLNP++ VG Q+ E Sbjct: 72 QVTGQAWFVQRDGRKVDLLAMPEAEKRTLRGNELAMIFQEPMTSLNPVLTVGEQIAESAR 131 Query: 119 WHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIA 178 H M A A +LE V IP + +R YP Q SGGMRQRVMIA+A+AC+P LLIA Sbjct: 132 LHLKMDRSTALAHARRMLELVEIPAAAQRVHEYPHQLSGGMRQRVMIALAMACNPTLLIA 191 Query: 179 DEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAP 238 DEPTTALDVTIQAQI+ L+ L++E GMS++F+TH+L V + D + MYAG+IVE A Sbjct: 192 DEPTTALDVTIQAQILALMGRLQKETGMSMLFVTHNLGVVAQYADAVAVMYAGRIVESAR 251 Query: 239 VEEILKTPLHPYTKGLLNSTLEIGSR------------GKKLVPIPGNPPNPTKHPSGCK 286 V ++ P HPYT+GLL + R +KLV IPG +P P GC Sbjct: 252 VHDLFARPEHPYTRGLLACLPGVARRQAQATDHAIAAGRRKLVAIPGQVSSPLAPPPGCA 311 Query: 287 FHPRCSFAMEICQREEPPLVNISENHRVAC 316 F PRC+ C P L V C Sbjct: 312 FAPRCTRQQADCTHAMPALEATGPRRMVRC 341 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: 272 Number of extensions: 11 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: 355 Length adjustment: 28 Effective length of query: 296 Effective length of database: 327 Effective search space: 96792 Effective search space used: 96792 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