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_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 254 bits (649), Expect = 4e-72 Identities = 133/254 (52%), Positives = 170/254 (66%), Gaps = 2/254 (0%) Query: 4 LLNVNNLKVEFHRVEGIV--KAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 +LNV +L ++F+ E KAV IS+K+ KG LGIVGESGSGKSV+ S++RL + Sbjct: 1 MLNVEHLNIDFYNQEEKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDER 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 + GE F LL L+ E+R IRG IS+IFQ PMTSLNP+ G QV E I+ HR Sbjct: 61 AAKITGEIDFEDISLLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHR 120 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 + EA++ I L V +P K F +YP Q SGG +QRVMIAMAL+C PKLLIADEP Sbjct: 121 KVDQAEAKKHTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEP 180 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 TTALDVT+Q I++LL +LK+E M++IFI+HDL V D + MY G+IVE+ P + Sbjct: 181 TTALDVTVQKTILQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKS 240 Query: 242 ILKTPLHPYTKGLL 255 I + P HPYTKGLL Sbjct: 241 IFENPQHPYTKGLL 254 Score = 205 bits (521), Expect = 2e-57 Identities = 109/245 (44%), Positives = 165/245 (67%), Gaps = 8/245 (3%) Query: 14 FHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73 F + VKAVD +++++ GE+LG+VGESG GK+ ++LRLI GE IF G Sbjct: 326 FGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTS----GEIIFNG 381 Query: 74 KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNE-EARERA 132 +++ + K LR +R KDI IIFQ+P SLNP + +G ++EP+ H+L +N+ E +++ Sbjct: 382 ENITHIGKTALRKLR-KDIQIIFQDPYASLNPKLSIGQSILEPLQVHKLYRNDSERKQKV 440 Query: 133 IELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQ 192 +ELL++VG+ E + F YP +FSGG RQRV+IA ALA PK +I DE +ALDV++QAQ Sbjct: 441 LELLDKVGLKE--EHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQ 498 Query: 193 IMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTK 252 ++ L+++L+ E+G++ IFI+HDL+V + DRI+ M GKI EE E+I P YT+ Sbjct: 499 VLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKAAYTQ 558 Query: 253 GLLNS 257 L+ + Sbjct: 559 KLIEA 563 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: 475 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 568 Length adjustment: 32 Effective length of query: 292 Effective length of database: 536 Effective search space: 156512 Effective search space used: 156512 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: 51 (24.3 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