GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  263 bits (673), Expect = 9e-75
 Identities = 165/504 (32%), Positives = 266/504 (52%), Gaps = 26/504 (5%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           +L  +NITK F  V A ++V+  ++ GEV AL+GENGAGK+TLM IL G Y    G + L
Sbjct: 15  VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131
            G  +    PR A + G+ ++ Q   L  NL+  ENI L  EP+   G +       +  
Sbjct: 75  FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLG-LRAGPAKARIR 133

Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191
            L  +  + +DP  KV  L+  ++Q V I KAL  DA+I+I+DEPT+ +  +E++ LF  
Sbjct: 134 ALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFAT 193

Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSI- 250
           +R   N G SVI+ISH+L E+  I+DRV+V+R G+ V E    + D D L  LMVG  + 
Sbjct: 194 LREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADVV 253

Query: 251 ---------DQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGL 301
                        ++ R   T       G++  SLD            +  G++ G+ G+
Sbjct: 254 PAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLD------------LAAGQITGLAGV 301

Query: 302 VGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQM 361
            G G+  L + + G    ++ G + + G      SPR+A+  GI  +PEDR   G I   
Sbjct: 302 SGNGQAALSDLVSGLITPQS-GSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADF 360

Query: 362 SVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQK 421
            +  N  L +   +   R  G +D +  ++  ++ I   +++ P P   +  LSGGN QK
Sbjct: 361 DLTENAILETYATRFSHR--GWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQK 418

Query: 422 VVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSD 481
           ++L + L   P+++L ++P RG+D+ A + +++ +++    G  V+++S +L EI+ +SD
Sbjct: 419 LILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSD 478

Query: 482 RILVMSEGRKTAEFLREEVTEEDL 505
            I V+SEGR +  F R     E+L
Sbjct: 479 VIHVISEGRLSPGFARGSKQPEEL 502


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: 548
Number of extensions: 27
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 523
Length of database: 522
Length adjustment: 35
Effective length of query: 488
Effective length of database: 487
Effective search space:   237656
Effective search space used:   237656
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:

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