Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 302 bits (774), Expect = 2e-86 Identities = 168/497 (33%), Positives = 284/497 (57%), Gaps = 8/497 (1%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65 ++++++++K F VA V L ++ G + AL+GENGAGKSTLM I++G+ +P GE+ + Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 66 KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKKKIL 124 +GK ++P A GI M+HQ L+ ++ ENI +G E +++ + + + Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 Query: 125 ELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184 EL R ++++P+ + ++S+ ++Q VEI K + +DILI DEPT+ +T E+ L I Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244 + +L +GK I+ ITHK++E+ A+AD + V R G I + L +MVGR +S Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304 + D++L ++DL + K +S D+ AGEI+G+AG+ G+G+T + + Sbjct: 263 QLFPLRETPIGDLLLTVRDLTLDG-----VFKDVSFDLHAGEILGIAGLMGSGRTNVAET 317 Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364 I G+T SG I L K + P E+ + EDR GL ++V EN+ + Sbjct: 318 IFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL- 376 Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424 P + GF+ + + ++ ++ V+ +LSGGNQQKA++AR + NP L Sbjct: 377 -PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRL 435 Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484 LI+ +PTRG+DVGA I++ + EG AV++IS EL E+L +SDR+ V+H+G++ G Sbjct: 436 LILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495 Query: 485 VSPETTTKQELGILMVG 501 + T++++ L G Sbjct: 496 LDRSEATQEKVMQLASG 512 Score = 90.1 bits (222), Expect = 2e-22 Identities = 58/265 (21%), Positives = 136/265 (51%), Gaps = 12/265 (4%) Query: 246 ITEKAAAQPKDV----VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTEL 301 +++ + QP+ + +LEI +++ K G + + + L VR G ++ + G +G G++ L Sbjct: 7 VSQPPSLQPQTLEEPYLLEIVNIS-KGFPGVVALADVQLRVRPGTVLALMGENGAGKSTL 65 Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361 +K I G+ + D+G I+L K I + P + + + ++ + L+ M++AENI + Sbjct: 66 MKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELN---LMPHMSIAENIWIG 122 Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421 + ++ +++ +++ EL+ + E +LS +Q IA+ + + Sbjct: 123 ---REQLNSLHMVNHREMHRCTAELLARLRINLDPE-EQVGNLSIAERQMVEIAKAVSYD 178 Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481 D+LI+ +PT + + ++ + + +GK ++ I+ +++E+ ++D +AV DG Sbjct: 179 SDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHY 238 Query: 482 QGIVSPETTTKQELGILMVGGNINE 506 G+ ++ L +MVG +++ Sbjct: 239 IGLQRADSMNSDSLISMMVGRELSQ 263 Lambda K H 0.315 0.135 0.365 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: 586 Number of extensions: 26 Number of successful extensions: 7 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: 506 Length of database: 517 Length adjustment: 35 Effective length of query: 471 Effective length of database: 482 Effective search space: 227022 Effective search space used: 227022 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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