Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 283 bits (724), Expect = 1e-80 Identities = 168/498 (33%), Positives = 288/498 (57%), Gaps = 17/498 (3%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 P+++L+N+ K F ++A N +L AGE+ AL+GENGAGK+TLM IL G Y D G ++ Sbjct: 9 PLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVM 68 Query: 81 L---DGKPVEITE--PRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDED 135 + G V++ P+ A GIG++HQ L +L+ +NI +G E LF + Sbjct: 69 VRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTE-----SLFARKF 123 Query: 136 ELNRQAAAIFARMR---LDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192 ++ A + M+ L++D V +L V +Q VEI KAL D+R+L++DEPTA L Sbjct: 124 SRSKARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLT 183 Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252 E LF ++ L A+G+ I++ISHKM E+ +DRV+V+R G+ +A +P + + Sbjct: 184 PQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKL 243 Query: 253 ISMMVGRALDGEQRIPPDTSRNDVVLEVRGLNRGR-AIRDVSFTLRKGEILGFAGLMGAG 311 +MVG A+ +R P + +V + GR I +V+ +LRKGEI+G AG+ G G Sbjct: 244 AELMVGHAVQMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGVSGNG 303 Query: 312 RTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQAN 371 ++ +A+ + G + AG + + G + + + A A+ G+ + EDR H G+ M V+ N Sbjct: 304 QSMLAKVLSGLEEPTAGAVTL-GSQPLKANAAAAIQSGVARIPEDRHHDGIVGAMSVEEN 362 Query: 372 IALSSMGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKW 429 + L + + + R G + IR+ AQ ++ I+ +RLLSGGN QKIV+A+ Sbjct: 363 LVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLART 422 Query: 430 LLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMC 489 L ++ I+ +P+RG+DVGA +++++ L ++G +++IS +L E+ ++S R+ V+ Sbjct: 423 LDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIH 482 Query: 490 EGRITGELARADATQEKI 507 G ++ +A + ++++ Sbjct: 483 RGHVSEPMASEELDKKQV 500 Score = 88.6 bits (218), Expect = 5e-22 Identities = 64/225 (28%), Positives = 106/225 (47%), Gaps = 11/225 (4%) Query: 291 DVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIK-----SPADA 345 +V+ L GEI+ G GAG+T + +FG + G +++ + +P A Sbjct: 28 NVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAA 87 Query: 346 VAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIK 405 + GIG + + HF LA + NI L + F R + R Q ++ ++ Sbjct: 88 LEAGIGMVHQ---HFTLAENLTGLENIVLGTESLFARK--FSRSKARAKLQELMQSSGLE 142 Query: 406 TPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465 ++ + L+ G +Q++ I K L RD IL DEPT + ++ L LA +G Sbjct: 143 V-DLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKLLAAKG 201 Query: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510 AI+ IS ++ EVL S RV V+ GRI +L + + K+ +L Sbjct: 202 MAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAEL 246 Score = 80.1 bits (196), Expect = 2e-19 Identities = 58/234 (24%), Positives = 115/234 (49%), Gaps = 7/234 (2%) Query: 38 LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQAL 97 ++N L GE+ L G +G G+S L K+LSG+ + +G + L +P++ Q+ Sbjct: 281 IENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVTLGSQPLKANAAAAIQS- 339 Query: 98 GIGIIHQELN---LMNHLSAAQNIFIG--REPR-KAMGLFIDEDELNRQAAAIFARMRLD 151 G+ I ++ + ++ +S +N+ + R+P + GL + R AI A Sbjct: 340 GVARIPEDRHHDGIVGAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRC 399 Query: 152 MDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGV 211 P L+ Q + +A+ L + +++ +P+ L+ A++ R +++ + +G Sbjct: 400 SGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGA 459 Query: 212 GIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQ 265 G++ IS +DEL Q++DR++V+ G + +E + MM G + GEQ Sbjct: 460 GVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGLMMAGHSAKGEQ 513 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: 545 Number of extensions: 33 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 520 Length of database: 515 Length adjustment: 35 Effective length of query: 485 Effective length of database: 480 Effective search space: 232800 Effective search space used: 232800 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 24 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