Alignments for a candidate for rbsA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Paraburkholderia bryophila 376MFSha3.1

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate H281DRAFT_03878 H281DRAFT_03878 xylose ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Burk376:H281DRAFT_03878
          Length = 519

 Score =  430 bits (1106), Expect = e-125
 Identities = 232/506 (45%), Positives = 334/506 (66%), Gaps = 13/506 (2%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPD--YEGQI 69
           LL  R I K F GV A++ + L +  GE   L GENGAGKSTLMK+L+GVYP   ++G+I
Sbjct: 5   LLTMRGIVKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDGEI 64

Query: 70  FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129
             EGK ++  + R+ +  GI +I QEL LVP LS AENIFL  E     G + Y  M+++
Sbjct: 65  TWEGKPLKATSIRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMYQR 124

Query: 130 ASKLFSKLGVN-IDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQL 188
           A +L  +LG++ I+    V +     QQ++ IAKAL+  AK++I+DEP+S++   E   L
Sbjct: 125 ADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAIL 184

Query: 189 FNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGR 248
            +I+R LK  G + +YISH+L+E+  + D + V+RDGR V   P+     D+++ LMVGR
Sbjct: 185 LDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGR 244

Query: 249 SIDQFFIKERATITDEIFRVEGIKLWSLDR-KKLLVDDVSFYVRKGEVLGIYGLVGAGRT 307
            I   F +E   I D IF    +  + +   ++  V DVSF +R+GE+LG+ GLVGAGRT
Sbjct: 245 EIKNLFPREPHPIGDVIFEARNVTCFDVTNPRRKRVSDVSFELRRGEILGVAGLVGAGRT 304

Query: 308 ELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNI 367
           EL++AIFGA+PG +E  V + GK +KI +P DA++ GIG+VPEDRK  G++  +SV HNI
Sbjct: 305 ELMQAIFGAYPGVSEATVVMEGKTVKIRAPIDAIRAGIGMVPEDRKRHGIVPGLSVGHNI 364

Query: 368 TLPSVVMKLIVRKF---GLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVL 424
           TL       ++++F   G IDS  E + + + +++L+++   P   + +LSGGNQQK VL
Sbjct: 365 TLA------VLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPMLSIASLSGGNQQKAVL 418

Query: 425 AKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRIL 484
            + L   PKVL+LDEPTRG+DV AK EIYKLI ++A  GM +VMVSSELPE+L +SDR+L
Sbjct: 419 TRMLLTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVL 478

Query: 485 VMSEGRKTAEFLREEVTEEDLLKAAI 510
           V+ EG    +F+ + +T+ED+L AAI
Sbjct: 479 VIGEGELRGDFVNDGLTQEDILSAAI 504



 Score = 91.7 bits (226), Expect = 6e-23
 Identities = 65/234 (27%), Positives = 121/234 (51%), Gaps = 8/234 (3%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHP-GRTEGKVFIGGKEIKIHSPRDAV 341
           +D +   V  GE +G+ G  GAG++ L++ + G +P G  +G++   GK +K  S RD  
Sbjct: 21  LDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDGEITWEGKPLKATSIRDTE 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 ISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAILLDIVRDLKR 193

Query: 462 SGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVK 515
            G+  V +S +L E+ A+ D I V+ +GR  A      +T + ++   + R +K
Sbjct: 194 RGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGREIK 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: 622
Number of extensions: 39
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