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 3609459 Dshi_2843 ABC transporter related (RefSeq)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Dino:3609459 Length = 548 Score = 236 bits (602), Expect = 2e-66 Identities = 163/488 (33%), Positives = 251/488 (51%), Gaps = 26/488 (5%) Query: 7 LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66 ++ ++KA+ V A +D + + G++H + G NGAGKST +SIL G + DAG I + Sbjct: 26 IELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIK 85 Query: 67 GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR--T 124 G + A+ AGI M+ Q + + TV EN+ LG E G ++ R Sbjct: 86 GQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAE---EGALLRPSLAKARKLL 142 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 REL + E +V + + LSV Q VEI KA ++I+DEPT + EA LF+ Sbjct: 143 RELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFR 202 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQE- 243 + L A+G I+ ++H+L E+ + D S+ R G + + AD + L +VG++ Sbjct: 203 ILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVGRKV 262 Query: 244 LTRIDHKVGRECAANTCLQVDNLSRAGE-----FHDISLQLRQGEILGIYGLMGSGRSEF 298 L R+D + A L VD+L + ISLQ+R GE+LGI G+ G+G+SE Sbjct: 263 LLRVDKTPAQPGA--PILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSEL 320 Query: 299 LNCIYGLTVADSGSVTLQGKPMPI----GLPKATINAGMSLVTEDRKDSGLVLTGSILSN 354 L + G+ A +G VT+ G+ + + K G++ V EDR+ GL++ N Sbjct: 321 LEVLGGMRPA-TGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWEN 379 Query: 355 IALS-----AYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVL 409 +A AY R L++ R AE + R ++ L + SGGNQQK+VL Sbjct: 380 VAFGYHDDPAYNR---GLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVL 436 Query: 410 AKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIA 469 A+ + P LL +PTRG+D GA + I+ + G A ++VS E E+L LSDR+A Sbjct: 437 AREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVA 496 Query: 470 VFKGGRLV 477 V GR++ Sbjct: 497 VMFDGRIM 504 Score = 85.9 bits (211), Expect = 3e-21 Identities = 61/221 (27%), Positives = 110/221 (49%), Gaps = 8/221 (3%) Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333 DIS+++ G I GI G G+G+S ++ +YG AD+G + ++G+ I +A I AG+ Sbjct: 43 DISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIKGQKTEIPDSQAAIRAGI 102 Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYK-RLSSWSLINARKETQLAEDMVKRLQIKTTSL 392 +V + K LV ++L N+ L A + L SL ARK L ++ + ++ Sbjct: 103 GMVFQHFK---LVENFTVLENVVLGAEEGALLRPSLAKARK---LLRELSEEYELNVAPD 156 Query: 393 ELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAI 452 L + +S G+QQ+V + K L + L+ DEPT + ++ +L+ G I Sbjct: 157 AL-IEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRILEGLKAEGKTII 215 Query: 453 VVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALLRL 493 +++ + E++ +D ++V + G + S E L L Sbjct: 216 LITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAEL 256 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: 644 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: 495 Length of database: 548 Length adjustment: 35 Effective length of query: 460 Effective length of database: 513 Effective search space: 235980 Effective search space used: 235980 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