Alignments for a candidate for HSERO_RS05250 in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Rhodobacter viridis JA737

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_110806166.1 C8J30_RS12430 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_003217355.1:WP_110806166.1
          Length = 530

 Score =  286 bits (733), Expect = 1e-81
 Identities = 190/524 (36%), Positives = 285/524 (54%), Gaps = 25/524 (4%)

Query: 1   MQEDKETSTTGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAG 60
           M    ET     AA +    P I LR + K F  V A  +    +  G +H ++GENGAG
Sbjct: 1   MASATETGRQATAAPAPRP-PAIELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAG 59

Query: 61  KSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFI 120
           KSTLM IL G Y+ D+G+IL+DG+P  I + + A   GIG++ Q   L+ + S  +N+ +
Sbjct: 60  KSTLMSILYGFYRADAGEILIDGRPTVIPDSQSAIRAGIGMVFQHFKLVPNFSVLENVIL 119

Query: 121 GREPRKAMGLFIDEDELNRQAAAIFAR-MRLDMDPSTPVGELTVARQQMVEIAKALSFDS 179
           G E    +   + +    R+  A  AR   LD+DP   V EL+V  QQ VEI KAL   +
Sbjct: 120 GAEDGALLRPSLAKA---RKTLADLARDYELDVDPDALVEELSVGHQQRVEILKALYRHA 176

Query: 180 RVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYI 239
            +LI+DEPT  L   E   LFRI+R L+AQG  I+ I+HK+ E+ +I D VSVMR G+ +
Sbjct: 177 DILILDEPTGVLTPDEADHLFRILRGLKAQGKTILLITHKLREIMEITDEVSVMRRGEMV 236

Query: 240 ATVPMQETSMDTIISMMVGR-ALDGEQRIPPDTSRNDVVLEVRGLNRGRA-----IRDVS 293
           ATV   +TS + +  +MVGR  L    + P +  R   VL V  L+   A     ++ ++
Sbjct: 237 ATVTTADTSPEQLAELMVGRKVLLHVPKGPANPGRE--VLRVSDLHVTDALGVERLKGIN 294

Query: 294 FTLRKGEILGFAGLMGAGRTEVARAIFG-ADPLEAGEIIIHG------GKAVIKSPADAV 346
            T+R GEILG AG+ G G++E+ + + G A    +G I + G      GK         +
Sbjct: 295 LTIRAGEILGIAGVAGNGQSELLQVLGGFAKGTVSGMIAVEGAQIPAAGKGATGQTRRQI 354

Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIAL---SSMGRFTRVGFMDQRAIREAAQMYVRQLA 403
             GI ++ EDR H GL +      NIA    S+        FMD  AI    +  + +  
Sbjct: 355 --GISHVPEDRHHLGLILDFAAWENIAFGYHSAPEYQANALFMDNDAILRDTEGKMDRFD 412

Query: 404 IKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAE 463
           ++ P     A+  SGGNQQKIV+A+ + R+  +L   +PTRG+D+GA   I++ +  L +
Sbjct: 413 VRPPDPSLPAKSFSGGNQQKIVLAREIERNPVLLLVGQPTRGVDIGAIEFIHRRIVELRD 472

Query: 464 QGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKI 507
            G A++++S EL E+L +S R+ VM +G+I GE   A+  + ++
Sbjct: 473 AGAAVLLVSVELDEILSLSDRIAVMFDGQIMGERLPAETNEREL 516



 Score =  106 bits (264), Expect = 2e-27
 Identities = 73/244 (29%), Positives = 126/244 (51%), Gaps = 14/244 (5%)

Query: 278 LEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIH 333
           +E+RG+++     +A +D+S  +R G I G  G  GAG++ +   ++G    +AGEI+I 
Sbjct: 22  IELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEILID 81

Query: 334 GGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM-GRFTRVGFMDQR-AI 391
           G   VI     A+  GIG + +   HF L     V  N+ L +  G   R      R  +
Sbjct: 82  GRPTVIPDSQSAIRAGIGMVFQ---HFKLVPNFSVLENVILGAEDGALLRPSLAKARKTL 138

Query: 392 REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAK 451
            + A+ Y  +L +   ++ ++   LS G+QQ++ I K L R  DIL  DEPT  +     
Sbjct: 139 ADLARDY--ELDVDPDALVEE---LSVGHQQRVEILKALYRHADILILDEPTGVLTPDEA 193

Query: 452 SEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLA 511
             ++++L  L  QGK I++I+ +L E++ ++  V VM  G +   +  AD + E++ +L 
Sbjct: 194 DHLFRILRGLKAQGKTILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAELM 253

Query: 512 TQRE 515
             R+
Sbjct: 254 VGRK 257



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 61/239 (25%), Positives = 115/239 (48%), Gaps = 12/239 (5%)

Query: 34  GVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRD-SGDILLDGKPVEITEP- 91
           GV  L      + AGE+  + G  G G+S L+++L G  +   SG I ++G  +      
Sbjct: 286 GVERLKGINLTIRAGEILGIAGVAGNGQSELLQVLGGFAKGTVSGMIAVEGAQIPAAGKG 345

Query: 92  ---RQAQALGIGIIHQE---LNLMNHLSAAQNIFIGREPR---KAMGLFIDEDELNRQAA 142
              +  + +GI  + ++   L L+   +A +NI  G       +A  LF+D D + R   
Sbjct: 346 ATGQTRRQIGISHVPEDRHHLGLILDFAAWENIAFGYHSAPEYQANALFMDNDAILRDTE 405

Query: 143 AIFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
               R  +   DPS P    +   QQ + +A+ +  +  +L++ +PT  ++   I  + R
Sbjct: 406 GKMDRFDVRPPDPSLPAKSFSGGNQQKIVLAREIERNPVLLLVGQPTRGVDIGAIEFIHR 465

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
            I +L+  G  ++ +S ++DE+  ++DR++VM DG+ +      ET+   +  +M G A
Sbjct: 466 RIVELRDAGAAVLLVSVELDEILSLSDRIAVMFDGQIMGERLPAETNERELGLLMAGVA 524


Lambda     K      H
   0.320    0.135    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: 623
Number of extensions: 29
Number of successful extensions: 9
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: 520
Length of database: 530
Length adjustment: 35
Effective length of query: 485
Effective length of database: 495
Effective search space:   240075
Effective search space used:   240075
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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