Align TM0028, 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 WP_011386731.1 AMB_RS22185 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >NCBI__GCF_000009985.1:WP_011386731.1 Length = 533 Score = 131 bits (330), Expect = 3e-35 Identities = 98/254 (38%), Positives = 141/254 (55%), Gaps = 16/254 (6%) Query: 22 VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKP-LTLVDGKIFLRVNGEFVE 80 V+AV G+SF + + E + +VGESG GK+ + I + P T G I R++G E Sbjct: 20 VQAVKGVSFTLAKGETLALVGESGSGKSVTALSILQLLPYPRATHPRGSI--RLDG--AE 75 Query: 81 LSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESH-GIDEEELLDKARR 139 L + RK G I ++ Q M +L P +E V + E H G+ L D+ Sbjct: 76 LVGAPEPAL-RKVRGGRIAMVFQEPMTSLNPLHSIEAQVGEVLELHLGLRGSTLRDRVVE 134 Query: 140 RFEEVGLDPLWIKRY---PFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVL 196 VG+ P KR P ELSGG RQR +IA+A P +LIADEPT+ALDV Q + Sbjct: 135 LLSLVGI-PEPEKRLGALPHELSGGQRQRVMIAMALAGEPDILIADEPTTALDVTIQAQI 193 Query: 197 LKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQ 256 L +L ++ + + +++FITHD+ VR++ADR+ +M AG+IVE P+ + + P HPYTQ Sbjct: 194 LALLKGLQAR-LGMALLFITHDLGIVRKMADRVCVMNAGEIVESGPLPQVFDAPAHPYTQ 252 Query: 257 GLFNSVLTPEPEVK 270 L L EP+ K Sbjct: 253 RL----LAAEPKGK 262 Score = 130 bits (328), Expect = 6e-35 Identities = 87/243 (35%), Positives = 131/243 (53%), Gaps = 22/243 (9%) Query: 22 VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVE- 80 VKAVDG+S ++ IGVVGESG GKTTL + L L+D + G +E Sbjct: 297 VKAVDGISLDLKRGHTIGVVGESGSGKTTLGLAL-------LRLLDSDGEISFGGTRIES 349 Query: 81 LSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVR-----HLAESHGIDEEELLD 135 +S+ T ++R ++ ++ Q +L P + + + V H H + + L+ Sbjct: 350 MSAGTLRPLRR-----QMQMVFQDPYGSLSPRMSVGQIVGEGLEVHEPAMHAAERDRLIA 404 Query: 136 KARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKV 195 A EEVGLDP RYP E SGG RQR IA A +L P ++ DEPTSALDV Q Sbjct: 405 AA---LEEVGLDPATRDRYPHEFSGGQRQRIAIARALVLKPKFIVLDEPTSALDVSVQAQ 461 Query: 196 LLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYT 255 ++ +L ++ + + + +FI+HD+ VR +AD +++M GK+VE + L + P YT Sbjct: 462 IVDLLRDLQARHAL-AYLFISHDLRVVRALADDLLVMKDGKVVEAGRADELFKAPRTAYT 520 Query: 256 QGL 258 + L Sbjct: 521 RAL 523 Lambda K H 0.321 0.138 0.405 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: 444 Number of extensions: 15 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: 330 Length of database: 533 Length adjustment: 32 Effective length of query: 298 Effective length of database: 501 Effective search space: 149298 Effective search space used: 149298 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: 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