Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Koxy:BWI76_RS19640 Length = 506 Score = 437 bits (1123), Expect = e-127 Identities = 225/502 (44%), Positives = 336/502 (66%), Gaps = 8/502 (1%) Query: 15 SSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQR 74 S S ++ + N+ K FPGV ALDN ++ +HALMGENGAGKSTL+K L G+YQ+ Sbjct: 6 SERSGEYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQK 65 Query: 75 DSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDE 134 DSG IL G+ ++ ++A GI ++HQELNL+ S N+++GR P K G+F+D+ Sbjct: 66 DSGSILFQGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GVFVDQ 123 Query: 135 DELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNA 194 D++ R AIF + +D+DP VG L+V++ QM+EIAKA S++++++IMDEPT++L Sbjct: 124 DKMYRDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEK 183 Query: 195 EIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIIS 254 E+ LF+IIR L+ +G GIVYISHKM+E+ Q+ D ++++RDG++IAT P++ MD II+ Sbjct: 184 EVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIA 243 Query: 255 MMVGRALDGEQRIP-PDTSRNDVVLEVRGLN--RGRAIRDVSFTLRKGEILGFAGLMGAG 311 MMVGR+L+ QR P + +V+LEVR L R +IRD+SF L KGEILG AGL+GA Sbjct: 244 MMVGRSLN--QRFPNKENKPGEVILEVRNLTSLRQPSIRDISFDLHKGEILGIAGLVGAK 301 Query: 312 RTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQAN 371 RT++ +FG G I +HG K S +A+ HG ++E+R+ G+ +D+ N Sbjct: 302 RTDIVETLFGIREKAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLDIGFN 361 Query: 372 IALSSMGRF-TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWL 430 +S++ ++ +VG +D ++ Q + + +KTP Q LSGGNQQK++I +WL Sbjct: 362 SLISNIKKYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGQHTQIGSLSGGNQQKVIIGRWL 421 Query: 431 LRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCE 490 L +IL DEPTRGIDVGAK EIY+L+ LA++ K I++ISSE+PE+L ++ R+LVM Sbjct: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDRILVMSN 481 Query: 491 GRITGELARADATQEKIMQLAT 512 G + G + TQ +I++LA+ Sbjct: 482 GLVAGIVETKTTTQNEILRLAS 503 Score = 73.2 bits (178), Expect = 2e-17 Identities = 59/247 (23%), Positives = 117/247 (47%), Gaps = 16/247 (6%) Query: 275 DVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEI 330 + +LE+ +N+ +A+ +V+ +R I G GAG++ + + +FG ++G I Sbjct: 11 EYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSI 70 Query: 331 IIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FMDQR 389 + G + S +A+ +GI + ++ L + V N+ L GR+ G F+DQ Sbjct: 71 LFQGQEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWL---GRYPTKGVFVDQD 124 Query: 390 AIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGID 447 + + +L I ++ +AR+ LS Q I IAK + I+ DEPT + Sbjct: 125 KMYRDTKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181 Query: 448 VGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKI 507 + ++K++ L E+G IV IS ++ E+ ++ + ++ +G+ +KI Sbjct: 182 EKEVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241 Query: 508 MQLATQR 514 + + R Sbjct: 242 IAMMVGR 248 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: 620 Number of extensions: 26 Number of successful extensions: 8 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: 506 Length adjustment: 35 Effective length of query: 485 Effective length of database: 471 Effective search space: 228435 Effective search space used: 228435 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