Alignments for a candidate for PS417_12065 in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Rhodobacter viridis JA737

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_110806166.1 C8J30_RS12430 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_003217355.1:WP_110806166.1
          Length = 530

 Score =  258 bits (660), Expect = 3e-73
 Identities = 170/488 (34%), Positives = 258/488 (52%), Gaps = 15/488 (3%)

Query: 3   RPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGS 62
           RP  ++   ++K++  V A +D  + +R G++H + G NGAGKST +SIL G  + DAG 
Sbjct: 18  RPPAIELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGE 77

Query: 63  ILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNR 122
           IL++G P        A+ AGI M+ Q  + +P  +V EN+ LG E      +  + A  R
Sbjct: 78  ILIDGRPTVIPDSQSAIRAGIGMVFQHFKLVPNFSVLENVILGAED--GALLRPSLAKAR 135

Query: 123 RT-RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQT 181
           +T  +L    E DVD  + +  LSV   Q VEI KA      ++I+DEPT  +   EA  
Sbjct: 136 KTLADLARDYELDVDPDALVEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADH 195

Query: 182 LFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241
           LF+ +R L AQG  I+ ++H+L E+ +I D+ S+ R G  V +   AD   + L   +VG
Sbjct: 196 LFRILRGLKAQGKTILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAELMVG 255

Query: 242 QE----LTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSE 297
           ++    + +     GRE    + L V +         I+L +R GEILGI G+ G+G+SE
Sbjct: 256 RKVLLHVPKGPANPGREVLRVSDLHVTDALGVERLKGINLTIRAGEILGIAGVAGNGQSE 315

Query: 298 FLNCIYGLTVAD-SGSVTLQGKPMPIGLPKAT----INAGMSLVTEDRKDSGLVLTGSIL 352
            L  + G      SG + ++G  +P     AT       G+S V EDR   GL+L  +  
Sbjct: 316 LLQVLGGFAKGTVSGMIAVEGAQIPAAGKGATGQTRRQIGISHVPEDRHHLGLILDFAAW 375

Query: 353 SNIAL---SAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVL 409
            NIA    SA +  ++   ++     +  E  + R  ++     LP  S SGGNQQK+VL
Sbjct: 376 ENIAFGYHSAPEYQANALFMDNDAILRDTEGKMDRFDVRPPDPSLPAKSFSGGNQQKIVL 435

Query: 410 AKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIA 469
           A+ +   PV LL  +PTRG+D GA + I+  + +    G A ++VS E  E+L LSDRIA
Sbjct: 436 AREIERNPVLLLVGQPTRGVDIGAIEFIHRRIVELRDAGAAVLLVSVELDEILSLSDRIA 495

Query: 470 VFKGGRLV 477
           V   G+++
Sbjct: 496 VMFDGQIM 503



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 68/222 (30%), Positives = 111/222 (50%), Gaps = 10/222 (4%)

Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333
           DIS+++R G I GI G  G+G+S  ++ +YG   AD+G + + G+P  I   ++ I AG+
Sbjct: 39  DISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEILIDGRPTVIPDSQSAIRAGI 98

Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYK-RLSSWSLINARKE-TQLAEDMVKRLQIKTTS 391
            +V +  K   LV   S+L N+ L A    L   SL  ARK    LA D    L +   +
Sbjct: 99  GMVFQHFK---LVPNFSVLENVILGAEDGALLRPSLAKARKTLADLARDY--ELDVDPDA 153

Query: 392 LELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAA 451
           L   V  +S G+QQ+V + K L      L+ DEPT  +       ++ +L      G   
Sbjct: 154 L---VEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADHLFRILRGLKAQGKTI 210

Query: 452 IVVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALLRL 493
           ++++ +  E++ ++D ++V + G +V   T    S E L  L
Sbjct: 211 LLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAEL 252


Lambda     K      H
   0.319    0.135    0.381 

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: 608
Number of extensions: 27
Number of successful extensions: 8
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: 495
Length of database: 530
Length adjustment: 35
Effective length of query: 460
Effective length of database: 495
Effective search space:   227700
Effective search space used:   227700
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 24 2021. 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