Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 256 bits (654), Expect = 1e-72 Identities = 162/492 (32%), Positives = 261/492 (53%), Gaps = 23/492 (4%) Query: 23 IALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLD 82 + L + K++PG LA D + GE+HAL+GENGAGKSTLMKI+ GV Q D+G+I Sbjct: 9 LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQ 68 Query: 83 GKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAA 142 G+ V + +P QA+ GIG++ Q +L LS A+NI + + +L + Sbjct: 69 GERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAG-----TPKQLEPKIR 123 Query: 143 AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRI 202 + R + ++P V L++ +Q VEI + L D R+LI+DEPT+ L E ELF Sbjct: 124 EVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVT 183 Query: 203 IRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALD 262 +R L A+G I++ISHK++E+R + +V+R G+ E S + +MVG A Sbjct: 184 LRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAEG 243 Query: 263 GEQRIPPDTSRNDVVLEVRGLN------RGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316 E P R L V L+ G ++++V +R GEI+G AG+ G G+ E+ Sbjct: 244 LEAEYPKSEGRAP-FLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQDELL 302 Query: 317 RAIFGADPLEAGE---IIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIA 373 + G L+A + I G P HG+ ++ +R G M + N Sbjct: 303 ALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSLADNGL 362 Query: 374 LSSMGRFTRVGFMDQRAIREA-----AQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428 L++ + + G ++Q IR A+ +++ A+KTP + A LSGGN QK ++ + Sbjct: 363 LTA---YQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGR 419 Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488 +L+ +L PT G+DVGA + I++ L L + G AI++IS +L E+ ++S R+ + Sbjct: 420 EILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAAL 479 Query: 489 CEGRITGELARA 500 +GR++ + A A Sbjct: 480 SDGRLSPQRATA 491 Score = 93.6 bits (231), Expect = 2e-23 Identities = 65/219 (29%), Positives = 110/219 (50%), Gaps = 9/219 (4%) Query: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351 + +++ GEI G GAG++ + + I+G +AGEI G + ++ PA A GIG Sbjct: 27 IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGIG 86 Query: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQ 411 + + HF L + V NIAL+ +G + IRE +Q Y L ++ Sbjct: 87 MVFQ---HFSLFETLSVAENIALA-LGAKAGTPKQLEPKIREVSQRYGMPL-----EPQR 137 Query: 412 QARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMI 471 LS G +Q++ I + L++D +L DEPT + E++ L LA +G +I+ I Sbjct: 138 LVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSILFI 197 Query: 472 SSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510 S +L EV + V+ GR++GE A+ + ++ +L Sbjct: 198 SHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARL 236 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: 590 Number of extensions: 39 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: 518 Length adjustment: 35 Effective length of query: 485 Effective length of database: 483 Effective search space: 234255 Effective search space used: 234255 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