GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pseudovibrio axinellae Ad2

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  282 bits (721), Expect = 2e-80
 Identities = 167/499 (33%), Positives = 285/499 (57%), Gaps = 13/499 (2%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           LL  +NITK F  ++A  NV L ++ GE+ AL+GENGAGK+TLM IL G Y   EG++ +
Sbjct: 10  LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMV 69

Query: 72  EGK-----EVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKM 126
                   ++    P+ A E GI ++ Q   L  NL+  ENI L  E +         K 
Sbjct: 70  RTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFA-RKFSRSKA 128

Query: 127 FEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETE 186
             +  +L    G+ +D   +V  L+  ++Q V I KAL  DA+I+++DEPT+ +  +E++
Sbjct: 129 RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESD 188

Query: 187 QLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMV 246
            LFN ++ L  +G ++I+ISH++ E+   +DRV V+R GR V + P  + D  KL  LMV
Sbjct: 189 SLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELMV 248

Query: 247 GRSIDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGR 306
           G ++ Q   +E     +EI   +G+   S    + L+++V+  +RKGE++G+ G+ G G+
Sbjct: 249 GHAV-QMAEREPGNPGEEILVFKGV---SAGEGRELIENVNLSLRKGEIIGLAGVSGNGQ 304

Query: 307 TELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHN 366
           + L + + G     T G V +G + +K ++   A+++G+  +PEDR   G++  MSV  N
Sbjct: 305 SMLAKVLSGLEE-PTAGAVTLGSQPLKANAAA-AIQSGVARIPEDRHHDGIVGAMSVEEN 362

Query: 367 ITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAK 426
           + L   + K   ++FGL+     ++  +  I+  +I+   P  +   LSGGN QK+VLA+
Sbjct: 363 LVLEE-IRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLAR 421

Query: 427 WLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVM 486
            L  +P ++L  +P+RG+DV A +++++ + E    G GV+++S +L E+  +SDRI V+
Sbjct: 422 TLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVI 481

Query: 487 SEGRKTAEFLREEVTEEDL 505
             G  +     EE+ ++ +
Sbjct: 482 HRGHVSEPMASEELDKKQV 500



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 59/229 (25%), Positives = 115/229 (50%), Gaps = 8/229 (3%)

Query: 28  VNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEVRFRNPREAQEN 87
           + NV L + KGE+  L G +G G+S L K+L+G+     G + L  + ++  N   A ++
Sbjct: 281 IENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVTLGSQPLK-ANAAAAIQS 339

Query: 88  GIALIPQELD---LVPNLSSAENIFLS--REPVNE-FGVIEYQKMFEQASKLFSKLGVNI 141
           G+A IP++     +V  +S  EN+ L   R+P  + FG++ + ++ ++A +      +  
Sbjct: 340 GVARIPEDRHHDGIVGAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRC 399

Query: 142 DPKTKVEDL-STSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNIIRSLKNEGK 200
                V  L S    Q + +A+ L  +  I++  +P+  +    T  +   ++  ++ G 
Sbjct: 400 SGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGA 459

Query: 201 SVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249
            V+ IS  L+E+F+++DR+ V+  G        EE D  ++  +M G S
Sbjct: 460 GVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGLMMAGHS 508



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 60/238 (25%), Positives = 121/238 (50%), Gaps = 17/238 (7%)

Query: 285 DVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGK-----EIKIHSPRD 339
           +V+  +  GE++ + G  GAG+T L+  +FG H    EG+V +        +++  +P+ 
Sbjct: 28  NVNLDLHAGEIVALLGENGAGKTTLMNILFG-HYVADEGRVMVRTSSGTLVDLEPGAPQA 86

Query: 340 AVKNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLE-KEIVRSFIE 398
           A++ GIG+V +    A     ++ L NI L +    L  RKF    ++ + +E+++S   
Sbjct: 87  ALEAGIGMVHQHFTLAE---NLTGLENIVLGTE--SLFARKFSRSKARAKLQELMQSSGL 141

Query: 399 KLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISE 458
           ++++        V  L+ G +Q+V + K L    ++L+LDEPT  +       ++  +  
Sbjct: 142 EVDLDLR-----VSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKL 196

Query: 459 MAVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKV 516
           +A  GM ++ +S ++ E+L  SDR+ V+  GR  A+    +     L +  +  +V++
Sbjct: 197 LAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELMVGHAVQM 254


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: 595
Number of extensions: 31
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 523
Length of database: 515
Length adjustment: 35
Effective length of query: 488
Effective length of database: 480
Effective search space:   234240
Effective search space used:   234240
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 24 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