Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate YP_001313054.1 Smed_4316 ABC transporter-like protein
Query= TCDB::Q7BSH4 (512 letters) >NCBI__GCF_000017145.1:YP_001313054.1 Length = 528 Score = 370 bits (950), Expect = e-107 Identities = 218/508 (42%), Positives = 306/508 (60%), Gaps = 18/508 (3%) Query: 14 TGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN 73 T A IL +S+ F GV AL +V L G + AL+GENGAGKSTL+K+L+G+Y Sbjct: 15 TEPARPILAAEAVSKSFGGVAALKDVRFDLRSGEIHALMGENGAGKSTLMKVLSGVYADY 74 Query: 74 EGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQT 133 EG + VDG F+S + A AG+ IHQE L EL VA+NIFLG +D + Sbjct: 75 EGTVRVDGEIARFSSVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVVAGLFVDRKA 134 Query: 134 MNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEI 193 ++ LL L +DP R+ L + ++ LV IA+ALS+EARI+IMDEPT+ALS E Sbjct: 135 SLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSSGEC 194 Query: 194 DDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSR----RPVRGVSRKTPQDE 249 LF+IVR L G I++ISH+ DE+ +++D VF R R RP+ G+ +D Sbjct: 195 RRLFKIVRQLAADGVGIVYISHRIDEVMQLSDRVTVF-RDGRHVWTRPMAGLD----EDT 249 Query: 250 IVRMMVGRDVENVFPKIDVAIGGPVLEIRNYS--------HRTEFRDISFTLRKGEILGV 301 I+ MVGR++ + P PVL + S R + +SF + GEILG+ Sbjct: 250 IIAAMVGRNLLDAHPVNRPKGAEPVLSVSGLSLAVAGRHGWRDVLKGVSFDVHAGEILGI 309 Query: 302 YGLIGAGRSELSQSLFGITKPL-SGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLA 360 GL+GAGR+E+ +++F + G++ L+G + I SP+DA R G V E+R GL Sbjct: 310 GGLLGAGRTEILETVFASNDGVRGGEIRLDGIAVDIRSPRDARRLGFALVTEDRKAKGLH 369 Query: 361 LPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQK 420 L I N+ LP + R +R G E ALA + E L +R A GTLSGGNQQK Sbjct: 370 LQESIRDNVALPLVGRLARFGLRSFERERALASRAVEALGVRCAGTDQTAGTLSGGNQQK 429 Query: 421 VVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSD 480 VVIGKWLAT P+V++LDEPT+GID+G+K ++ + +LAA+GL+I++VSSELPE++ ++D Sbjct: 430 VVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLVFKLAADGLAIVVVSSELPELLLLAD 489 Query: 481 RVLVMKEGLSAGIFERAELSPEALVRAA 508 R+LVM EG G+ R E S E +++ A Sbjct: 490 RILVMAEGRQTGLISREEASEERIMQLA 517 Score = 93.6 bits (231), Expect = 2e-23 Identities = 66/224 (29%), Positives = 106/224 (47%), Gaps = 5/224 (2%) Query: 287 RDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAG 346 +D+ F LR GEI + G GAG+S L + L G+ G + ++G+ S +DA AG Sbjct: 38 KDVRFDLRSGEIHALMGENGAGKSTLMKVLSGVYADYEGTVRVDGEIARFSSVRDAEAAG 97 Query: 347 IVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAAL 406 I + +E L + + N+ L R F+ AR RL + Sbjct: 98 IAIIHQELN---LVPELGVADNIFL-GRERVVAGLFVDRKASLEAARGLLNRLGIELDP- 152 Query: 407 SVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSII 466 VG L G QQ V I K L+ +++I+DEPT + G + + +LAA+G+ I+ Sbjct: 153 EARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSSGECRRLFKIVRQLAADGVGIV 212 Query: 467 MVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 +S + E++ +SDRV V ++G A L + ++ A G Sbjct: 213 YISHRIDEVMQLSDRVTVFRDGRHVWTRPMAGLDEDTIIAAMVG 256 Lambda K H 0.320 0.137 0.382 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: 625 Number of extensions: 26 Number of successful extensions: 7 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: 512 Length of database: 528 Length adjustment: 35 Effective length of query: 477 Effective length of database: 493 Effective search space: 235161 Effective search space used: 235161 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