Alignments for a candidate for xylG in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_06298 H281DRAFT_06298 L-arabinose ABC transporter ATP-binding protein

Query= TCDB::A6LW11
         (525 letters)



>FitnessBrowser__Burk376:H281DRAFT_06298
          Length = 519

 Score =  393 bits (1009), Expect = e-113
 Identities = 218/501 (43%), Positives = 324/501 (64%), Gaps = 14/501 (2%)

Query: 6   LEMRDIVKEFFGVKALDGVTLKVKKGEIHALCGENGAGKSTLMKVLSGEHPAGSYSGKII 65
           L   +I K F GV+ALDGV+  V  G++H L GENGAGKSTL+K+L GE+   S  G+++
Sbjct: 12  LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDS--GRVM 69

Query: 66  FEGKELSQTSIKDSESVGIAIIHQELALIKQLSIAENIFLGNEIGARGLVNFSEQLNKTN 125
            +GKE+  TS   S + GIA+IHQEL  +  L++AEN+ LG    + G VN  +      
Sbjct: 70  IDGKEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSFGWVNKRDAKRFVR 129

Query: 126 ELLNRVKLNVNPLTRAGDLGIGHQQLVEIAKALSKNAKLLILDEPSASLSEGEVEVLMGI 185
           E L  + + ++P  +   L I  +Q+VEI KAL +NA+++ LDEP++SLS  E EVL  +
Sbjct: 130 ERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKL 189

Query: 186 LDDLRRDGVTCIYISHKLNEVTRICDNVTVIRDGSTIGQVPISE-IDQDKLVQMMVGREM 244
           + DLR D    IYISH+++E+  +CD  T+ RDG  I   P  E + +D +V  MVGRE+
Sbjct: 190 VRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVSRDTIVSEMVGREI 249

Query: 245 KNLFPREEHKIGEEFFEIKNFNVLDPFNKNIKRVKNASFTLRRGEILGISGLVGSGRTEM 304
            +++   E  +GE  F  K         +     + ASF +RRGEI+G  GLVG+GR+E+
Sbjct: 250 SDIYNYSERPLGEVRFAAKAI-------EGHALSQPASFEVRRGEIVGFFGLVGAGRSEL 302

Query: 305 VASIYGSFQGQKSGEVYFEGKKIDIKNPNDALSKGIAMVPEDRKKDGIIAGMSVAKNMTM 364
           +  +YG+ + +K GE+  +GK I +K+  +A+  GI + PEDRK++GI+A  +V++N+ +
Sbjct: 303 MHLVYGT-EHKKGGELVLDGKTIRVKSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINI 361

Query: 365 SNLVKYKRPLNVIDKDKEMMDVLKFIDEIKIKTASTELAIKNLSGGNQQKVILAKNLLAE 424
           S    Y R    +D+ KE     +FI  +KIKT S    I+ LSGGNQQK IL++  LAE
Sbjct: 362 SCRRHYLRAGVFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR-WLAE 420

Query: 425 P--KILILDEPTRGIDVGAKYEIYKLIFKLAKQGISIIMVSSELPEVLGISDRVLVMNEG 482
           P  K++ILDEPTRGIDVGAK+EIY +I++LA++G +I+M+SSELPEVLG+SDR++VM +G
Sbjct: 421 PDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQG 480

Query: 483 EIKASLENNGLTQEMIMNYSV 503
            I   L     T++ +++ ++
Sbjct: 481 RIAGELSRKDATEQAVLSLAL 501



 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 57/261 (21%), Positives = 126/261 (48%), Gaps = 12/261 (4%)

Query: 256 GEEFFEIKNFNVLDPFNKNIKRVKNASFTLRRGEILGISGLVGSGRTEMVASIYGSFQGQ 315
           G E      F+ +      ++ +   SF +  G++ G+ G  G+G++ ++  + G +Q  
Sbjct: 5   GGEVSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQ-P 63

Query: 316 KSGEVYFEGKKIDIKNPNDALSKGIAMVPEDRKKDGIIAGMSVAKNMTMSNLVKYKRPLN 375
            SG V  +GK++   +   +++ GIA++ ++ +    +  ++VA+N+ +  L      +N
Sbjct: 64  DSGRVMIDGKEVRFTSAASSIAAGIAVIHQELQ---YVPDLTVAENLLLGQLPNSFGWVN 120

Query: 376 VIDKDKEMMDVLKFIDEIKIKTASTELAIKNLSGGNQQKVILAKNLLAEPKILILDEPTR 435
             D  + + + L+ +       A     ++ LS   +Q V + K LL   +++ LDEPT 
Sbjct: 121 KRDAKRFVRERLEAMGVALDPNAK----LRKLSIAQRQMVEICKALLRNARVIALDEPTS 176

Query: 436 GIDVGAKYEIYKLIFKLAKQGISIIMVSSELPEVLGISDRVLVMNEGEIKASLEN-NGLT 494
            +       ++KL+  L     ++I +S  + E+  + D   +  +G   AS     G++
Sbjct: 177 SLSHRETEVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVS 236

Query: 495 QEMIMNYSVGKKNEEVSESYS 515
           ++ I++  VG+   E+S+ Y+
Sbjct: 237 RDTIVSEMVGR---EISDIYN 254


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: 715
Number of extensions: 43
Number of successful extensions: 11
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: 525
Length of database: 519
Length adjustment: 35
Effective length of query: 490
Effective length of database: 484
Effective search space:   237160
Effective search space used:   237160
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.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources