Alignments for a candidate for rhaT' in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Phaeobacter inhibens BS107

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  275 bits (704), Expect = 2e-78
 Identities = 179/508 (35%), Positives = 278/508 (54%), Gaps = 18/508 (3%)

Query: 9   VTDSKTGDAPA---ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKI 65
           +   K G AP    +L ++ I++ F  V A D+VS  L PG V AL+GENGAGK+TL+ I
Sbjct: 1   MASDKMGQAPGLTPVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNI 60

Query: 66  LTGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTR 125
           L G Y  + G + + G P    + +AA+D GV  +HQ   L D LTV ENI LG  P   
Sbjct: 61  LFGQYMADTGGVELFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLG 120

Query: 126 FRTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPT 185
              +      +R +AL       +DP  ++  L++ +R  V I +AL  +ARI+I+DEPT
Sbjct: 121 L-GLRAGPAKARIRALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPT 179

Query: 186 AALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKT 245
           A L+ +E D LF  +R    +G +++FISHK  E+  I+D  +V  R  +      +  T
Sbjct: 180 AVLTPQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVL-RHGKLVAERQTADT 238

Query: 246 PQDEIVRMMVGRDVENVFPKIDVAIGGP-VLEIRNYSHRTE-----FRDISFTLRKGEIL 299
             D +  +MVG DV  V  K      GP +L++R+ +  +       R +S  L  G+I 
Sbjct: 239 DSDALAALMVGADV--VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQIT 296

Query: 300 GVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGL 359
           G+ G+ G G++ LS  + G+  P SG + L G      SP++AI AGI  +PE+R + G 
Sbjct: 297 GLAGVSGNGQAALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGT 356

Query: 360 ALPMPIFQNMTLPSLA-RTSRRGFL--RAANEFALARKYAERLDLRAAALSVPVGTLSGG 416
                + +N  L + A R S RG+L  RAA +F  A+      D+R       +  LSGG
Sbjct: 357 IADFDLTENAILETYATRFSHRGWLDWRAARDF--AKTVITGYDVRCPGPDTRIRLLSGG 414

Query: 417 NQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEII 476
           N QK+++G+ L  +P++I+ ++P +G+DIG+   VH  +++  A G +++++S +L EI+
Sbjct: 415 NMQKLILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIM 474

Query: 477 GMSDRVLVMKEGLSAGIFERAELSPEAL 504
            +SD + V+ EG  +  F R    PE L
Sbjct: 475 QLSDVIHVISEGRLSPGFARGSKQPEEL 502



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 76/245 (31%), Positives = 123/245 (50%), Gaps = 16/245 (6%)

Query: 273 PVLEIRNYSHR----TEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328
           PVL ++N + R    T   D+SF L  GE++ + G  GAG++ L   LFG     +G + 
Sbjct: 14  PVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73

Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL---PSLARTSRRGFLRA 385
           L G  +   +P+ A+  G+  V +      LA  + +++N+TL   P L    R G  +A
Sbjct: 74  LFGAPLPPGAPRAALDGGVGMVHQH---FTLADNLTVWENITLGVEPLLGLGLRAGPAKA 130

Query: 386 ANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDI 445
               ALA ++  ++D  A      V  L+ G +Q+V I K L    +++ILDEPT  +  
Sbjct: 131 RIR-ALAEQFHLKVDPNAK-----VSRLTVGERQRVEILKALYRDARILILDEPTAVLTP 184

Query: 446 GSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALV 505
               A+   + E    GLS+I +S +L E++ +SDRVLV++ G      + A+   +AL 
Sbjct: 185 QESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALA 244

Query: 506 RAATG 510
               G
Sbjct: 245 ALMVG 249


Lambda     K      H
   0.320    0.137    0.382 

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: 624
Number of extensions: 28
Number of successful extensions: 7
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: 512
Length of database: 522
Length adjustment: 35
Effective length of query: 477
Effective length of database: 487
Effective search space:   232299
Effective search space used:   232299
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
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