Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 178 bits (451), Expect = 3e-49 Identities = 101/263 (38%), Positives = 159/263 (60%), Gaps = 14/263 (5%) Query: 4 LVVKNLTKIFSL--GFFSKRR--IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRL 59 L +KNL + + G F K ++AV ++FEV E + LVGESG GKTT + ILRL Sbjct: 310 LQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRL 369 Query: 60 LPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAIS-- 117 + PTSGEI F G++I K +L + R+ + +FQDP+AS NP + +++ + + Sbjct: 370 IQPTSGEIIFNGENITHIGKT--ALRKLRKDIQIIFQDPYASLNPKLSIGQSILEPLQVH 427 Query: 118 -LLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLI 176 L N K++ LEL+ +VG+ ++ +YPH+ SGGQ+QR++IAR L+P I Sbjct: 428 KLYRNDSERKQKVLELLD----KVGLK-EEHFNRYPHEFSGGQRQRVVIARALALQPKFI 482 Query: 177 VADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 + DE S +D S + ++ L+++L+ E G + IFI+HDL + ++SD I VM G+I E Sbjct: 483 ICDESVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEE 542 Query: 237 GHPDKVVLEPTHEYTKLLVGSIP 259 G P+++ P YT+ L+ +IP Sbjct: 543 GFPEQIFYAPKAAYTQKLIEAIP 565 Score = 154 bits (390), Expect = 3e-42 Identities = 94/255 (36%), Positives = 145/255 (56%), Gaps = 10/255 (3%) Query: 20 KRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRL----LPPTSGEIYFEGKDIW 75 K +AVK +SF+VK+ ++ +VGESGSGK+ T+ I+RL +GEI FE + Sbjct: 17 KTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLL 76 Query: 76 KDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE--NKPSNKKEALELI 133 ++ E ++ +FQ+P S NP + + +AI L ++ KK + L Sbjct: 77 -NLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIALF 135 Query: 134 KESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGI 193 E P+ + YPHQISGGQKQR+MIA P L++ADEPT+ +D + + I Sbjct: 136 NEVQLP---RPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTI 192 Query: 194 IKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKL 253 ++LL +L++E+ ++IFI+HDLG+ ++D + VM GEIVE+G + P H YTK Sbjct: 193 LQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFENPQHPYTKG 252 Query: 254 LVGSIPKLYRKLEDL 268 L+ P R+L+ L Sbjct: 253 LLACRPSPNRQLKKL 267 Lambda K H 0.319 0.139 0.397 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: 423 Number of extensions: 13 Number of successful extensions: 6 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: 268 Length of database: 568 Length adjustment: 30 Effective length of query: 238 Effective length of database: 538 Effective search space: 128044 Effective search space used: 128044 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 (21.7 bits) S2: 50 (23.9 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