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 AZOBR_RS01940 AZOBR_RS01940 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__azobra:AZOBR_RS01940 Length = 636 Score = 169 bits (427), Expect = 2e-46 Identities = 96/240 (40%), Positives = 143/240 (59%), Gaps = 9/240 (3%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE-- 82 AV +VSF + E V LVGESG GKTT +K+++R L P +G++ F D+ E Sbjct: 344 AVDDVSFAIARGECVGLVGESGCGKTTLSKILMRALTPDAGDVRFNDHGRVVDVLGLEGA 403 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAIS--LLENKPSNKKEALELIKESLFRV 140 +L FRRKV VFQDPF S NP T++ I L+ + ++ E +KE + V Sbjct: 404 ALTAFRRKVQFVFQDPFGSLNP----RMTVFDIIEEPLVIHGIGDEAERAARVKELMGLV 459 Query: 141 GIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEEL 200 G+D + L +YPH SGGQ+QRI IAR LRP L++ DEP S +D S + ++ LL++L Sbjct: 460 GLDARH-LRRYPHSFSGGQRQRIGIARALALRPELLLLDEPVSALDVSIQAQVLNLLKDL 518 Query: 201 REEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPK 260 +E G + +F++H+L + Y++D I VM G IVE + + P H YT+ L+ ++P+ Sbjct: 519 KERLGLTYLFVSHNLAVVDYMADRILVMCRGRIVESAPREALFRNPVHPYTRALLAAVPE 578 Score = 152 bits (383), Expect = 2e-41 Identities = 87/255 (34%), Positives = 148/255 (58%), Gaps = 17/255 (6%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTS----GEIYFEGKDIWKDI 78 + AV+ VSF V+ V+LVGESGSGK+ A+ ILR+LP + G+I F+ I + + Sbjct: 22 VHAVRGVSFRVRAGSTVALVGESGSGKSVAAQSILRILPRNATIADGQILFDDGIINEGV 81 Query: 79 ---------KDRESLVEFRR-KVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKE 128 D ++ R ++ +FQ+P S +P + V + +A+ L + + ++ Sbjct: 82 GPVDIAGLKADGTAMRALRGGRISIIFQEPMTSLSPLHTVGDQVGEAVRLHQRVTA--RQ 139 Query: 129 ALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDA 187 A ++ L RV DPK L YP ++SGG +QR MIA + RP L++ADEPT+ +D Sbjct: 140 ARAQAEDMLRRVRFPDPKRALDTYPFELSGGLRQRAMIAMALVCRPALLIADEPTTALDV 199 Query: 188 SSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPT 247 + + I+KL+++L+ + G +++ ITHDLG+ ++D + VM G I+E G + + +P Sbjct: 200 TIQAQILKLIKDLQADLGMAVLLITHDLGVVANLADEVVVMHRGRIMESGTREDIFADPR 259 Query: 248 HEYTKLLVGSIPKLY 262 H Y K L+ ++P+ + Sbjct: 260 HPYLKALLRAVPRFH 274 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: 410 Number of extensions: 21 Number of successful extensions: 5 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: 636 Length adjustment: 31 Effective length of query: 237 Effective length of database: 605 Effective search space: 143385 Effective search space used: 143385 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