Alignments for a candidate for rbsA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudarthrobacter sulfonivorans Ar51

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_058930145.1 AU252_RS07280 sugar ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_001484605.1:WP_058930145.1
          Length = 506

 Score =  358 bits (919), Expect = e-103
 Identities = 207/505 (40%), Positives = 306/505 (60%), Gaps = 15/505 (2%)

Query: 6   EKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDY 65
           E +   LLE R +TK F GV A+  V LQ+  GEV  ++G+NGAGKSTL+K L+GV+   
Sbjct: 4   EDQPRPLLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVHQPD 63

Query: 66  EGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQK 125
            G+I  EGK++    P  A + GIA + QELD+V  LS AENIFL  E  +  GV+  +K
Sbjct: 64  GGEIRWEGKQITLPRPTAALDLGIATMYQELDVVDGLSVAENIFLGHER-STGGVLHVKK 122

Query: 126 MFEQASKLFSKLGV-NIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRE 184
               A  L  +LG  ++ P T+V  LS + +Q+V++A+ALS D K+IIMDEP++ +   E
Sbjct: 123 TNAIARTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILDSGE 182

Query: 185 TEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEG-PIEEFDHDKLVR 243
              LF ++R L  +G +V+YISHRLEEI +I DR+ V++DGR    G  + +    +L+R
Sbjct: 183 VSNLFRVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSVTDTQKSELIR 242

Query: 244 LMVGRSIDQFFIKERATITDE--IFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGL 301
           LM GR +   F + +    D   +  V+ ++L+    K      VS  VR GE+LG  GL
Sbjct: 243 LMTGRDVANVFPERKPVPADAPVVLDVDNLELYGHFEK------VSLTVRAGEILGFAGL 296

Query: 302 VGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQM 361
           VG+ R+E+LE I+GA    + G+V + GK ++  S   AV  GIGL PE+RK+ GLIL  
Sbjct: 297 VGSKRSEILETIYGARKA-SSGRVSVNGKALRPGSVTSAVNAGIGLSPEERKSQGLILDE 355

Query: 362 SVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQK 421
            +  N+TL +        + G ++   E+   R  I  L ++   P +    LSGGNQQK
Sbjct: 356 PLFKNVTLSTFER---FARMGYLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQK 412

Query: 422 VVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSD 481
           ++LA+WL     VLLLDEPTRG+DV A+SEIY LI ++A +G  +++VSSE+ E+L ++D
Sbjct: 413 ILLARWLVHGTSVLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLAD 472

Query: 482 RILVMSEGRKTAEFLREEVTEEDLL 506
            +LV+ +G+   +    ++ E  +L
Sbjct: 473 NVLVIDDGKVLTQTKASDIDEHGVL 497



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 60/250 (24%), Positives = 116/250 (46%), Gaps = 14/250 (5%)

Query: 11  VLLEARNITKTFPGVIAVNN---------VTLQIYKGEVCALVGENGAGKSTLMKILAGV 61
           V  E + +    P V+ V+N         V+L +  GE+    G  G+ +S +++ + G 
Sbjct: 252 VFPERKPVPADAPVVLDVDNLELYGHFEKVSLTVRAGEILGFAGLVGSKRSEILETIYGA 311

Query: 62  YPDYEGQIFLEGKEVRFRNPREAQENGIALIPQELD---LVPNLSSAENIFLSR-EPVNE 117
                G++ + GK +R  +   A   GI L P+E     L+ +    +N+ LS  E    
Sbjct: 312 RKASSGRVSVNGKALRPGSVTSAVNAGIGLSPEERKSQGLILDEPLFKNVTLSTFERFAR 371

Query: 118 FGVIEYQKMFEQASKLFSKLGVN-IDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEP 176
            G +        A +  + L +   DP      LS   QQ + +A+ L     ++++DEP
Sbjct: 372 MGYLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQKILLARWLVHGTSVLLLDEP 431

Query: 177 TSAIGKRETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEF 236
           T  +      +++++IR L   G ++I +S  +EE+  +AD V+V+ DG+ + +    + 
Sbjct: 432 TRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLADNVLVIDDGKVLTQTKASDI 491

Query: 237 DHDKLVRLMV 246
           D   ++ L++
Sbjct: 492 DEHGVLDLVM 501


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: 581
Number of extensions: 30
Number of successful extensions: 10
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: 506
Length adjustment: 35
Effective length of query: 488
Effective length of database: 471
Effective search space:   229848
Effective search space used:   229848
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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