Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 92.4 bits (228), Expect = 2e-23 Identities = 64/222 (28%), Positives = 102/222 (45%), Gaps = 20/222 (9%) Query: 3 ALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLL 62 A L+LK +DK + + A+ +L + G + VG +G GKST+++++ G+ + G L+ Sbjct: 2 AFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLI 61 Query: 63 WLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122 G++ T P + + ++ Q L P +T+ EN+ F R K+D + + Sbjct: 62 LDGRDITEVPP---SQRDLAMVFQSYALYPHMTVEENM----SFALRLAKVDPAIIQEKV 114 Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDAL-------TDT 175 KLNL + LS G +Q V I + + KV + DEP L T Sbjct: 115 KMAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRV 174 Query: 176 ETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDG 217 E SL R + G VY++H E + D V V RDG Sbjct: 175 EIASLHREL------GATTVYVTHDQVEAMTLADRVVVLRDG 210 Score = 70.9 bits (172), Expect = 7e-17 Identities = 53/205 (25%), Positives = 98/205 (47%), Gaps = 14/205 (6%) Query: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLAN 327 + VS ++ GE + G G G++ L++++ G G + LDG ++ T P Sbjct: 19 IKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILDGRDI-TEVPPSQRDL 77 Query: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTP 387 +V+ S L M+V+ENMS ALR ++ + A + + +TP Sbjct: 78 AMVFQSY-----ALYPHMTVEENMSF-ALRLAKVDPAIIQEKVKMAADKLNLTAYLQRTP 131 Query: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEI-YQLINQFKADGL 446 LSGG +Q+VAI R ++ PKV + DEP +D + ++ + + G Sbjct: 132 KA------LSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLHRELGA 185 Query: 447 SIILVSSEMPEVLGMSDRIIVMHEG 471 + + V+ + E + ++DR++V+ +G Sbjct: 186 TTVYVTHDQVEAMTLADRVVVLRDG 210 Lambda K H 0.318 0.137 0.380 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: 373 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 501 Length of database: 348 Length adjustment: 31 Effective length of query: 470 Effective length of database: 317 Effective search space: 148990 Effective search space used: 148990 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: 41 (21.7 bits) S2: 50 (23.9 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