GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS22465
          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.

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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:

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