GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 D-xylose transport
           ATP-binding protein XylG
          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 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