GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N2E2

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456
          Length = 518

 Score =  402 bits (1034), Expect = e-116
 Identities = 214/505 (42%), Positives = 327/505 (64%), Gaps = 7/505 (1%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP--DYEG 67
           + LL+   I KTF GV A+N + +++  GE   L GENGAGKSTLMK+L+ VYP   ++G
Sbjct: 3   DYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDG 62

Query: 68  QIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMF 127
           +I  +G+ ++ ++  E +  GI +I QEL LVP+LS AENIF+  E     G + Y  M 
Sbjct: 63  EILWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMI 122

Query: 128 EQASKLFSKLGV-NIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETE 186
            +A  L  +L V +++    V       QQ+V IAKAL+  A+++I+DEP+SA+ + E E
Sbjct: 123 HRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIE 182

Query: 187 QLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMV 246
            L +IIR LK +G + +YISH+L+E+  + D + V+RDG+ +    + +    K++  MV
Sbjct: 183 VLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMV 242

Query: 247 GRSIDQFFIKERATITDEIFRVEGIKLWSLDR-KKLLVDDVSFYVRKGEVLGIYGLVGAG 305
           GR +   +  E   + + IF       + +D  ++  VDD+SF +++GE+LGI GLVGAG
Sbjct: 243 GREMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAG 302

Query: 306 RTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLH 365
           RTEL+ A+FGA+PGR EG+V++ G++I   +P  +++ G+ +VPEDRK  G+I  + V  
Sbjct: 303 RTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQ 362

Query: 366 NITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLA 425
           NITL  +       K   ID++ E   +   I ++++KT SP+  + +LSGGNQQK VLA
Sbjct: 363 NITLAVLDN---YSKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLA 419

Query: 426 KWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILV 485
           K L  KP+VL+LDEPTRG+DV AK EIYKL+  +A  G+ ++MVSSEL E+L +SDR+LV
Sbjct: 420 KMLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLV 479

Query: 486 MSEGRKTAEFLREEVTEEDLLKAAI 510
           + +G+   +F+  E+T+E +L AA+
Sbjct: 480 IGDGQLRGDFINHELTQEQVLAAAL 504



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 57/239 (23%), Positives = 114/239 (47%), Gaps = 20/239 (8%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHP-GRTEGKVFIGGKEIKIHSPRDAV 341
           ++ +   VR GE +G+ G  GAG++ L++ +   +P G  +G++   G+ +K  S  +  
Sbjct: 21  LNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEILWDGQPLKAQSISETE 80

Query: 342 KNGIGLVPEDRKTAGLILQMSVLHNI------TLPSVVMKLIVRKFGLIDSQLEKEIVRS 395
             GI ++ ++     L+  +SV  NI      TLP   M      +  +  + E  +   
Sbjct: 81  AAGIVIIHQELT---LVPDLSVAENIFMGHELTLPGGRMN-----YPAMIHRAEALMREL 132

Query: 396 FIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKL 455
            +  +N+  P     V    GG QQ V +AK L  + ++L+LDEP+  +  +    +  +
Sbjct: 133 KVPDMNVSLP-----VSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVLLDI 187

Query: 456 ISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514
           I ++   G+  V +S +L E+ A+ D I V+ +G+  A     +++   ++   + R +
Sbjct: 188 IRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMVGREM 246


Lambda     K      H
   0.317    0.137    0.372 

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: 637
Number of extensions: 26
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: 523
Length of database: 518
Length adjustment: 35
Effective length of query: 488
Effective length of database: 483
Effective search space:   235704
Effective search space used:   235704
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: 41 (21.6 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