GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Dyella japonica UNC79MFTsu3.2

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein

Query= SwissProt::P37388
         (513 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3232
          Length = 513

 Score =  542 bits (1397), Expect = e-158
 Identities = 278/501 (55%), Positives = 364/501 (72%), Gaps = 3/501 (0%)

Query: 4   LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63
           L EM+ I K+FG VKA+D + LRL AGE + LCGENG+GKSTLMKVL G+YPHGS++GEI
Sbjct: 7   LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66

Query: 64  IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITH-NGIMDYDLMTLR 122
           ++ G+ ++A  +RD+ER GI IIHQEL LV +L+V ENIFLG+EIT   G MDYD M  +
Sbjct: 67  LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAK 126

Query: 123 CQKLLAQVSL-SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSIL 181
              LL ++ L  ++        G G QQL EIAKAL KQ +LLILDEPT+SLT  ET +L
Sbjct: 127 ADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVL 186

Query: 182 LDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGR 241
           L I+ DL++ G+ACIYISHKL+EV+ + DT+CVIRDG+HI T+    +  D +IT+MVGR
Sbjct: 187 LGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGR 246

Query: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301
           +L  LYP   H  G+ I    H T   PVN   KRV+DVSF L+RGEILGIAGLVGAGRT
Sbjct: 247 KLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRT 306

Query: 302 ETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNI 361
           E +  +FG + G+   +++++G+ + IR+   AI  G+ MVPEDRKR GIVP++ VG NI
Sbjct: 307 ELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNI 366

Query: 362 TLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLL 421
           TLA L+ +      +D   E   I   I + +VKT+SP L I RLSGGNQQKA+LA+ LL
Sbjct: 367 TLATLDHYAHA-GHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLL 425

Query: 422 LNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEG 481
             P++LILDEPTRG+D+GAK EIY+LI +L  QG+A++++SSE+PEVLG++DRVLVM EG
Sbjct: 426 ARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEG 485

Query: 482 KLKANLINHNLTQEQVMEAAL 502
           +L+ +  N  LTQEQV+ AA+
Sbjct: 486 RLRGDFPNQGLTQEQVLAAAI 506


Lambda     K      H
   0.319    0.137    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: 745
Number of extensions: 26
Number of successful extensions: 8
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: 513
Length of database: 513
Length adjustment: 35
Effective length of query: 478
Effective length of database: 478
Effective search space:   228484
Effective search space used:   228484
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.

Links

Downloads

Related tools

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:

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:

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