Align Xylose import ATP-binding protein XylG, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein
Query= TCDB::A6LW11 (525 letters) >FitnessBrowser__Phaeo:GFF2770 Length = 505 Score = 256 bits (654), Expect = 1e-72 Identities = 165/514 (32%), Positives = 272/514 (52%), Gaps = 14/514 (2%) Query: 1 MSEYILEMRDIVKEFFGVKALDGVTLKVKKGEIHALCGENGAGKSTLMKVLSGEHPAGSY 60 M++ +L ++ + K + GV A D V+ + GE+HAL GENGAGKSTL+K++ G S Sbjct: 1 MTQPLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDS- 59 Query: 61 SGKIIFEGKELSQTSIKDSESVGIAIIHQELALIKQLSIAENIFLGNEIGARGLVNFSEQ 120 GK++ G+ + + + + GIA++ Q +L L++AENI LG E L + + Q Sbjct: 60 -GKMLLHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGMETPP-ALRDLATQ 117 Query: 121 LNKTNELLNRVKLNVNPLTRAGDLGIGHQQLVEIAKALSKNAKLLILDEPSASLSEGEVE 180 + K +E L ++P GDL G +Q VEI + L ++ KLLI+DEP++ L+ EVE Sbjct: 118 IRKVSETYG---LPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVE 174 Query: 181 VLMGILDDLRRDGVTCIYISHKLNEVTRICDNVTVIRDGSTIGQVPISEIDQDKLVQMMV 240 +L L LR +G + +YISHKL E+ +CD+ T++R G +G+ SE + +MMV Sbjct: 175 ILFQTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMV 234 Query: 241 GREMKNLFPREEHKIGEEFFEIKNFNVLDPFNKNIKRVKNASFTLRRGEILGISGLVGSG 300 G ++ R +G+ +I +V P + +KN T+R+GEILG+ G+ G+G Sbjct: 235 GTALQTP-ERSGRALGDVALDISGLSVPAP-SAFGTALKNVHMTVRKGEILGVGGVAGNG 292 Query: 301 RTEMVASIYGSFQGQKSGEVYFEGKKIDIKNPNDALSKGIAMVPEDRKKDGIIAGMSVAK 360 + E++ + G + V +G I P GI PE+R MS+ + Sbjct: 293 QDELLGVLSGE-TTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTE 351 Query: 361 NMTMSNLVK---YKRPLNVIDKDKEMMDVLKFIDEIKIKTASTELAIKNLSGGNQQKVIL 417 N ++ + R +E + K I ++T E A ++LSGGN QK ++ Sbjct: 352 NAMLTAATREGLASRGFLKWGLAQEFAE--KVIKSFDVRTPGPENAARSLSGGNLQKFVI 409 Query: 418 AKNLLAEPKILILDEPTRGIDVGAKYEIYKLIFKLAKQGISIIMVSSELPEVLGISDRVL 477 + +L P +L++++PT G+D A I + + LA G ++I +S +L E++ I+D Sbjct: 410 GREVLQRPDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFA 469 Query: 478 VMNEGEIKASLENNGLTQEMIMNYSVGKKNEEVS 511 +NEG + A GL+ + I G EV+ Sbjct: 470 ALNEGRLSAPRPTAGLSVDEIGLMMGGAHGMEVA 503 Lambda K H 0.315 0.135 0.362 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: 606 Number of extensions: 34 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 525 Length of database: 505 Length adjustment: 35 Effective length of query: 490 Effective length of database: 470 Effective search space: 230300 Effective search space used: 230300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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