Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 354 bits (909), Expect = e-102 Identities = 197/489 (40%), Positives = 294/489 (60%), Gaps = 5/489 (1%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 + G+ K FPGVKALD+V F++ GE+ LLGENGAGKS+L+K L GVY AD G + Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRF--GLLRRKEMEKRA 126 +G ++ + A LGI ++QE +L+P + +A N+F+GREP+ G + M A Sbjct: 70 DGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEA 129 Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186 ++ G + R P++R VA QQ+V I +A+ +A++L+LDEPTA+L +E E LF Sbjct: 130 RRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFA 189 Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL 246 ++ +L+ GVS+I+++H + +V+ + DRIT+LR+G VG + ELV M+GR++ Sbjct: 190 VIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGRKV 249 Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306 D + R+ + +N IA +L+VR GEIVGLAGL+GSGR+E A + Sbjct: 250 DMSYSRE--RSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAV 307 Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ 366 FG P G I GK + P +A LG PE RK++G+ +VR+N++LA + Sbjct: 308 FGADPIRQGEIYIFGK-RLTGGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRR 366 Query: 367 RGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426 R + + +AER I +L I TP Q +FLSGGNQQK+++ +WL+ + I Sbjct: 367 AFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIF 426 Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486 DEPTRGIDVGA AEI LI++L G +L+ISSEL E++ DR +MR + E+ Sbjct: 427 DEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAH 486 Query: 487 AELSVPAIM 495 AE++ I+ Sbjct: 487 AEMTEERIL 495 Score = 63.9 bits (154), Expect = 1e-14 Identities = 59/238 (24%), Positives = 107/238 (44%), Gaps = 18/238 (7%) Query: 20 PGVKALD-----------NVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 PG ALD +++ +R GEI+ L G G+G+S + +A+ G +G I++ Sbjct: 261 PGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAVFGADPIRQGEIYI 320 Query: 69 EGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPKRFGL--LRRKEME 123 G+ ++ A++LG + + L +V DNL + + F R + E Sbjct: 321 FGKRLTG-GPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRRAFPARWYRADKAE 379 Query: 124 KRATELMASYGFSLDVREPLNRF-SVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVE 182 A +A + L +F S QQ + I + + AK+ I DEPT +D Sbjct: 380 ALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIFDEPTRGIDVGAKA 439 Query: 183 LLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKM 240 +F L+ L +G ++ ++ L ++ V DR V+R G G E+ + ++++ Sbjct: 440 EIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHAEMTEERILQL 497 Lambda K H 0.321 0.138 0.391 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: 582 Number of extensions: 25 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: 500 Length of database: 502 Length adjustment: 34 Effective length of query: 466 Effective length of database: 468 Effective search space: 218088 Effective search space used: 218088 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