Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 469 bits (1206), Expect = e-136 Identities = 251/492 (51%), Positives = 340/492 (69%), Gaps = 4/492 (0%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 ++ + N+ K FPGV+AL + Q + G V ALMGENGAGKSTLMKI++G+YQ D+G+I L Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 GKP+ P AQ GI +IHQELNLM H+S A+NI+IGRE ++ + ++ E++R Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHM-VNHREMHRCT 141 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 A + AR+R+++DP VG L++A +QMVEIAKA+S+DS +LIMDEPT+A+ E+A LF Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 II DL++QG GIVYI+HKM+E+ IAD V+V RDG YI + D++ISMMVGR L Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 Query: 262 DGEQRIP-PDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320 Q P +T D++L VR L +DVSF L GEILG AGLMG+GRT VA IF Sbjct: 262 S--QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319 Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380 G P +G+I + G I P A+ G L+EDRK GL + V N+ ++ + + Sbjct: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 Query: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440 T GF+ Q+A+R + ++L +KTPS+EQ LSGGNQQK ++A+WL+ + +L D Sbjct: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439 Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500 EPTRGIDVGAK+EIY+L+ LA +G A++MISSELPEVL MS RV+VM EG + G L R+ Sbjct: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499 Query: 501 DATQEKIMQLAT 512 +ATQEK+MQLA+ Sbjct: 500 EATQEKVMQLAS 511 Score = 100 bits (250), Expect = 1e-25 Identities = 62/221 (28%), Positives = 117/221 (52%), Gaps = 6/221 (2%) Query: 43 FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102 F+L AGE+ + G G+G++ + + + G+ SG I LDGK V I++P A G ++ Sbjct: 293 FDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALL 352 Query: 103 HQELNLMNH---LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTP-- 157 ++ L LS +N+ + P FI + L + ++R+ PS Sbjct: 353 TEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKT-PSLEQC 411 Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217 + L+ QQ +A+ L + R+LI+DEPT ++ AE++R+I L ++G+ ++ IS Sbjct: 412 IDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMIS 471 Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258 ++ E+ ++DRV VM +G+ + T+ E + + ++ + G Sbjct: 472 SELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 Score = 89.0 bits (219), Expect = 4e-22 Identities = 70/254 (27%), Positives = 119/254 (46%), Gaps = 11/254 (4%) Query: 267 IPPDTSRNDVVLEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGA 322 + P T +LE+ +++G A+ DV +R G +L G GAG++ + + I G Sbjct: 13 LQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGI 72 Query: 323 DPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTR 382 +AGEI + G V ++P A GI + ++ L M + NI + + Sbjct: 73 YQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQE---LNLMPHMSIAENIWIGRE-QLNS 128 Query: 383 VGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEP 442 + ++ R + + +L I E+Q LS +Q + IAK + D DIL DEP Sbjct: 129 LHMVNHREMHRCTAELLARLRINLDP-EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEP 187 Query: 443 TRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADA 502 T I + ++ ++ L QGK IV I+ ++ EV ++ V V +G G L RAD+ Sbjct: 188 TSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADS 246 Query: 503 -TQEKIMQLATQRE 515 + ++ + RE Sbjct: 247 MNSDSLISMMVGRE 260 Lambda K H 0.320 0.135 0.372 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: 600 Number of extensions: 33 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 520 Length of database: 517 Length adjustment: 35 Effective length of query: 485 Effective length of database: 482 Effective search space: 233770 Effective search space used: 233770 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: 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