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 Synpcc7942_2236 Synpcc7942_2236 ATPase
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__SynE:Synpcc7942_2236 Length = 554 Score = 126 bits (317), Expect = 1e-33 Identities = 80/242 (33%), Positives = 129/242 (53%), Gaps = 8/242 (3%) Query: 24 AVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSS 83 A+ GL + E +G+VGESG GK+ I + K F V G+ Sbjct: 20 ALQGLDLVVQPGESVGIVGESGSGKSVACLAIPGLLPKTARCSGQIAFRSVAGQSSRDLL 79 Query: 84 MTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESH-GIDEEELLDKARRRFE 142 + R+ G + I Q +++L P + + H + + E + + Sbjct: 80 TLPERELRQLRGDRLGFIFQEPLSSLNPVFSAGFQLLEAIQQHLPLSQAEAQQRVIALLQ 139 Query: 143 EVGL--DPLW----IKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVL 196 EV L +P ++RYP +LSGG RQR +IAIA NP LL+ADEPT+ALD Q + Sbjct: 140 EVQLIREPSQAAQILRRYPHQLSGGQRQRLMIAIALAANPDLLLADEPTTALDATVQASV 199 Query: 197 LKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQ 256 L++L ++++Q + ++IF++HD+ + ++ADR++++Y G++VE V +L P HPYTQ Sbjct: 200 LQLLRRLQQQRQM-AMIFVSHDLGVIAEVADRVVVLYRGQVVEQGRVADVLNSPQHPYTQ 258 Query: 257 GL 258 GL Sbjct: 259 GL 260 Score = 113 bits (282), Expect = 1e-29 Identities = 85/268 (31%), Positives = 148/268 (55%), Gaps = 29/268 (10%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 LL+ E + Y+ + +AV LSF + +G+VGESGCGK++L+ + V + Sbjct: 300 LLQVEQLGITYRGRSTAFQAVQNLSFTLPAGLTLGLVGESGCGKSSLARCL----VGLVP 355 Query: 65 LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMN-------ALMPTIRMEK 117 +G+I+L + + ++L S +RD + + + + P AA++ A++ +R+++ Sbjct: 356 ASEGQIWL--DQQPLDLRS-SRDRQRLRQTVQMVFQDPAAALDPRWTVGSAILEPLRIKQ 412 Query: 118 YVRHLAESHGIDEEELLDKARRRFE---EVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174 R ++ LL + +R + ++G RYP E SGG RQR IA A I Sbjct: 413 PRRDRTA-----DQRLLKQWLQRVDLPTDIG------DRYPHEFSGGQRQRICIARALIG 461 Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234 P LLI DE SALDV Q +L +L Q++ + + + +FI+HD+A VR ++DR+++M Sbjct: 462 QPRLLICDESVSALDVSVQAQILNLLKQLQAE-LGLTYLFISHDLAVVRYMSDRILVMNQ 520 Query: 235 GKIVEFAPVESLLEKPLHPYTQGLFNSV 262 G++ E +P E L ++P YT+ L ++ Sbjct: 521 GQLEEDSPTEQLFQRPQSDYTRRLIAAI 548 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: 427 Number of extensions: 18 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: 554 Length adjustment: 32 Effective length of query: 298 Effective length of database: 522 Effective search space: 155556 Effective search space used: 155556 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