Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 229 bits (583), Expect = 2e-64 Identities = 148/482 (30%), Positives = 251/482 (52%), Gaps = 16/482 (3%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 LL +++ K + + A + L L AG + AL G NGAGK+T ++IL G D G +++ Sbjct: 10 LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMV 69 Query: 66 NGAP-----VQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKAL 120 + ++ P AL AGI M+ Q +T ENI LG E A +KA Sbjct: 70 RTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA- 128 Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180 + +EL+ S +VD + +L+V + Q VEI KA D +++++DEPT+ + E+ Sbjct: 129 RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESD 188 Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240 +LF ++ L A+G I+++SH+++E+ +D ++ R G V + DR L +V Sbjct: 189 SLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELMV 248 Query: 241 GQELTRIDHKVGRECAANTCLQVDNLSRAGE----FHDISLQLRQGEILGIYGLMGSGRS 296 G + + + G L +S AGE +++L LR+GEI+G+ G+ G+G+S Sbjct: 249 GHAVQMAEREPGN--PGEEILVFKGVS-AGEGRELIENVNLSLRKGEIIGLAGVSGNGQS 305 Query: 297 EFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIA 356 + GL +G+VTL +P+ A I +G++ + EDR G+V S+ N+ Sbjct: 306 MLAKVLSGLEEPTAGAVTLGSQPLKAN-AAAAIQSGVARIPEDRHHDGIVGAMSVEENLV 364 Query: 357 LSAYKR--LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLS 414 L ++ + L+ + + A++ +K I+ + +SGGN QK+VLA+ L Sbjct: 365 LEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLD 424 Query: 415 TEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGG 474 EP +L +P+RG+D GA +++ L + G +++S + EL LSDRIAV G Sbjct: 425 QEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRG 484 Query: 475 RL 476 + Sbjct: 485 HV 486 Score = 82.0 bits (201), Expect = 4e-20 Identities = 62/212 (29%), Positives = 106/212 (50%), Gaps = 17/212 (8%) Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPI-----GLPKAT 328 +++L L GEI+ + G G+G++ +N ++G VAD G V ++ + G P+A Sbjct: 28 NVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAA 87 Query: 329 INAGMSLVTEDRKDSGLVLTGSILSNIAL---SAYKRLSSWSLINARKETQLAEDMVKRL 385 + AG+ +V + LTG L NI L S + R S S A+ + + ++ Sbjct: 88 LEAGIGMVHQ-HFTLAENLTG--LENIVLGTESLFARKFSRSKARAKLQELMQSSGLE-- 142 Query: 386 QIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFV 445 L+L V+ ++ G +Q+V + K L + L+ DEPT + +++ L Sbjct: 143 ----VDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKLLA 198 Query: 446 RGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV 477 G A I +S + E+L SDR+AV +GGR+V Sbjct: 199 AKGMAIIFISHKMAEVLGASDRVAVLRGGRIV 230 Lambda K H 0.319 0.135 0.381 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: 532 Number of extensions: 29 Number of successful extensions: 9 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: 495 Length of database: 515 Length adjustment: 34 Effective length of query: 461 Effective length of database: 481 Effective search space: 221741 Effective search space used: 221741 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