GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Herbaspirillum seropedicae SmR1

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter

Query= SwissProt::P37388
         (513 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22465 HSERO_RS22465 sugar ABC
           transporter
          Length = 518

 Score =  546 bits (1407), Expect = e-160
 Identities = 277/502 (55%), Positives = 377/502 (75%), Gaps = 3/502 (0%)

Query: 3   YLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGE 62
           YLLEMK I K+FG V+A++ + +++  GE V LCGENG+GKSTLMK+L G+YPHG++EGE
Sbjct: 4   YLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEGE 63

Query: 63  IIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEIT-HNGIMDYDLMTL 121
           I++ G+ +QA  +RDTE  GI IIHQEL LV EL+V ENIF+G+EIT   G M+Y  M  
Sbjct: 64  ILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPAMYR 123

Query: 122 RCQKLLAQVSL-SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180
           R ++L+ ++++  I+    V   G G QQLVEIAKALNK  RLLILDEP++SLT  E  +
Sbjct: 124 RAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIGV 183

Query: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 240
           LL II+DL+  G+AC+YISHKL+EV  + DTI VIRDG+HI T     M  D IIT MVG
Sbjct: 184 LLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMVG 243

Query: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300
           RE+TA+YP   H  G+ +L   ++T +   N   KRV+DVSFS++RGEILGIAGLVGAGR
Sbjct: 244 REITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVGAGR 303

Query: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360
           TE +  +FG + G++EG++ ++GK  D  +  ++I +G+ MVPEDRK  GIVP + VG+N
Sbjct: 304 TELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPDLDVGQN 363

Query: 361 ITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCL 420
           ITL  LN+F+ G S++D +AE K I + I +++VKT++P L I  LSGGNQQKA+LA+ L
Sbjct: 364 ITLTVLNRFSRG-SRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAVLAKML 422

Query: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480
           L  P++LILDEPTRG+D+GAK EIY+LI++L + G+A+I++SSEL EVLG+SDRVLV+ E
Sbjct: 423 LAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRVLVIGE 482

Query: 481 GKLKANLINHNLTQEQVMEAAL 502
           G+L+ + +N NL+QE V+ AA+
Sbjct: 483 GRLRGDFVNDNLSQETVLAAAI 504



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 62/237 (26%), Positives = 119/237 (50%), Gaps = 7/237 (2%)

Query: 18  KAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEEIQASHIRD 77
           K +D+V   +  GEI+ + G  G+G++ L+  + G Y  G YEG+++  G+    S    
Sbjct: 278 KRVDDVSFSVRRGEILGIAGLVGAGRTELVSAIFGAY-RGRYEGQVLLEGKPADTSSPLK 336

Query: 78  TERKGIAIIHQEL---ALVKELTVLENIFLG--NEITHNGIMDYDLMTLRCQKLLAQVSL 132
           + R+G+ ++ ++     +V +L V +NI L   N  +    +D        Q  + ++ +
Sbjct: 337 SIRRGLCMVPEDRKHHGIVPDLDVGQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRV 396

Query: 133 -SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQH 191
            + +P   +  L  G QQ   +AK L  Q ++LILDEPT  +     + +  +I +L + 
Sbjct: 397 KTATPFLPITSLSGGNQQKAVLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKA 456

Query: 192 GIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRELTALYP 248
           G+A I +S +L EV  +SD + VI +G+  G      +S++ ++   + + +    P
Sbjct: 457 GLAIIMVSSELAEVLGVSDRVLVIGEGRLRGDFVNDNLSQETVLAAAINQPVPQATP 513


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: 750
Number of extensions: 35
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: 513
Length of database: 518
Length adjustment: 35
Effective length of query: 478
Effective length of database: 483
Effective search space:   230874
Effective search space used:   230874
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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