Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 3608553 Dshi_1947 ABC transporter related (RefSeq)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Dino:3608553 Length = 514 Score = 293 bits (750), Expect = 1e-83 Identities = 181/494 (36%), Positives = 265/494 (53%), Gaps = 11/494 (2%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 PV+ L + KRF + A D F+L AGEV AL+GENGAGK+TLM IL G Y D G + Sbjct: 9 PVLRLDQITKRFGALTANDAISFDLHAGEVVALLGENGAGKTTLMNILFGHYTADEGTVE 68 Query: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140 + G+ + PR A A G+G++HQ L ++LS N+ +G P GL R+ Sbjct: 69 VFGQTLPPGVPRAALAAGVGMVHQHFTLADNLSVLDNVILGTVPLWRAGL--GSGAARRK 126 Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200 A+ L +DP VG L+V +Q VEI KAL D+R+LI+DEPTA L E LF Sbjct: 127 LRALAEDFGLQVDPEARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQEAEALF 186 Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260 +R A+G+ +++ISHK+ E+ +A RV V+R G+ + V ET + MMVG Sbjct: 187 ATLRRAVARGMSVIFISHKLHEVMSVAHRVVVLRHGRVVGRVATDETDRHALAEMMVGAE 246 Query: 261 LDGEQRIPPD-----TSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEV 315 + P + + V + RG G +RDVS TLR G+I G AG+ G G+ + Sbjct: 247 ITAPAPRPATPGAALMTLDRVCTDARGTATG--LRDVSLTLRAGQITGLAGVSGNGQAAL 304 Query: 316 ARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALS 375 A I G AG + + + SP A+A GIG + EDR G + N L Sbjct: 305 ADLIGGLIAPVAGALRLGNAEVADWSPRAALAQGIGRIPEDRHKTGTIADFTLTENAILE 364 Query: 376 S--MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRD 433 + +F+R G+M A A+ + ++ P E RLLSGGN QK+++ + L Sbjct: 365 AYPKAQFSRSGWMRWGAAESFARDVIASYDVRCPGPETPIRLLSGGNMQKLILGRVLEDG 424 Query: 434 CDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRI 493 I+ ++P RG+D+GA + + + L A + G A+++IS +L EVL +S + VM EGR+ Sbjct: 425 PRIVLANQPVRGLDIGAVTYVQEQLIAARDGGAAVLLISEDLDEVLALSDVIHVMSEGRL 484 Query: 494 TGELARADATQEKI 507 + E AR T ++ Sbjct: 485 SPEFARGSMTPAQL 498 Score = 93.6 bits (231), Expect = 2e-23 Identities = 66/229 (28%), Positives = 114/229 (49%), Gaps = 16/229 (6%) Query: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351 +SF L GE++ G GAG+T + +FG + G + + G P A+A G+G Sbjct: 29 ISFDLHAGEVVALLGENGAGKTTLMNILFGHYTADEGTVEVFGQTLPPGVPRAALAAGVG 88 Query: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMD---QRAIREAAQMYVRQLAIKTPS 408 + + HF LA + V N+ L ++ + R G +R +R A+ + Q Sbjct: 89 MVHQ---HFTLADNLSVLDNVILGTVPLW-RAGLGSGAARRKLRALAEDFGLQ------- 137 Query: 409 VEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466 V+ +AR+ LS G +Q++ I K L RD IL DEPT + ++ L +G Sbjct: 138 VDPEARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQEAEALFATLRRAVARGM 197 Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515 +++ IS +L EV+ ++HRV+V+ GR+ G +A + + + ++ E Sbjct: 198 SVIFISHKLHEVMSVAHRVVVLRHGRVVGRVATDETDRHALAEMMVGAE 246 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: 584 Number of extensions: 23 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: 520 Length of database: 514 Length adjustment: 35 Effective length of query: 485 Effective length of database: 479 Effective search space: 232315 Effective search space used: 232315 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 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