Aligments for a candidate for rbsA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for rbsA in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate BPHYT_RS32815 BPHYT_RS32815 sugar ABC transporter

Query= TCDB::Q9X051
         (523 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS32815 BPHYT_RS32815 sugar ABC
           transporter
          Length = 519

 Score =  428 bits (1100), Expect = e-124
 Identities = 230/508 (45%), Positives = 335/508 (65%), Gaps = 13/508 (2%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP--DYEG 67
           + L+  R I K F GV A++ + L +  GE   L GENGAGKSTLMK+L+GVYP   ++G
Sbjct: 3   QALMTMRGIVKAFSGVKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDG 62

Query: 68  QIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMF 127
           +I  EG+ ++  + R+ +  GI +I QEL LVP LS AENIFL  E     G + Y  M+
Sbjct: 63  EIIWEGEPLKAASVRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMY 122

Query: 128 EQASKLFSKLGVN-IDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETE 186
           ++A +L  +LG++ I+    V +     QQ++ IAKAL+  AK++I+DEP+S++   E  
Sbjct: 123 QRADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIR 182

Query: 187 QLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMV 246
            L +I+R LK  G + +YISH+L+E+  + D + V+RDGR V   P+     D+++ LMV
Sbjct: 183 ILLDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMV 242

Query: 247 GRSIDQFFIKERATITDEIFRVEGIKLWSLDR-KKLLVDDVSFYVRKGEVLGIYGLVGAG 305
           GR I   F +E   I D IF    +  + +   ++  V+DVSF +R GE+LG+ GLVGAG
Sbjct: 243 GREIKNLFPREPHPIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGLVGAG 302

Query: 306 RTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLH 365
           RTEL++AIFGA+PG +E  V + GK +KI +P DA++ GIG+VPEDRK  G++  +SV H
Sbjct: 303 RTELMQAIFGAYPGVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPGLSVGH 362

Query: 366 NITLPSVVMKLIVRKF---GLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKV 422
           NITL       ++++F   G IDS  E + + + +++L+++   P   + +LSGGNQQK 
Sbjct: 363 NITLA------VLQRFASGGRIDSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKA 416

Query: 423 VLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDR 482
           VL + L   PKVL+LDEPTRG+DV AK EIYKLI ++A  GM +VMVSSELPE+L +SDR
Sbjct: 417 VLTRMLLTNPKVLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDR 476

Query: 483 ILVMSEGRKTAEFLREEVTEEDLLKAAI 510
           +LV+ EG    +F+ + +T+ED+L AAI
Sbjct: 477 VLVIGEGELRGDFVNDGLTQEDILSAAI 504



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 64/234 (27%), Positives = 120/234 (51%), Gaps = 8/234 (3%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHP-GRTEGKVFIGGKEIKIHSPRDAV 341
           +D +   V  GE +G+ G  GAG++ L++ + G +P G  +G++   G+ +K  S RD  
Sbjct: 21  LDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDGEIIWEGEPLKAASVRDTE 80

Query: 342 KNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLN 401
           + GI ++ ++     L+ ++SV  NI L + +     R       Q   E++R    +L 
Sbjct: 81  RAGIIIIHQELM---LVPELSVAENIFLGNEITLPGGRMNYAAMYQRADELLR----ELG 133

Query: 402 IKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAV 461
           I   +  Q V N  GG+QQ + +AK L  + K+L+LDEP+  +  +    +  ++ ++  
Sbjct: 134 ISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIRILLDIVRDLKR 193

Query: 462 SGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVK 515
            G+  V +S +L E+ A+ D I V+ +GR  A      +T + ++   + R +K
Sbjct: 194 RGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMVGREIK 247


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: 625
Number of extensions: 38
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: 519
Length adjustment: 35
Effective length of query: 488
Effective length of database: 484
Effective search space:   236192
Effective search space used:   236192
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources