Alignments for a candidate for HSERO_RS05250 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Acidovorax sp. GW101-3H11

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  369 bits (946), Expect = e-106
 Identities = 217/495 (43%), Positives = 303/495 (61%), Gaps = 11/495 (2%)

Query: 23  IALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLD 82
           +  RNV K F  V  L    F L  G V+ L+GENGAGKSTLMKIL+G     +G++++D
Sbjct: 5   VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64

Query: 83  GKPVEITEP----RQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELN 138
           G    +  P    R A+A GI +IHQE NL + L+ AQNIF+G E ++  GLF+D+  + 
Sbjct: 65  GA---VRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKR--GLFLDDKAMR 119

Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
            +     A++ L +DP T V +L VA +Q+VEIA+AL+ ++R+LIMDEPTA L   E   
Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           LF ++  L+A GV I+YISHK+DE+ +  D V VMRDG  +A       +   + ++MVG
Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVG 239

Query: 259 RAL-DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVAR 317
           R L D      P        + VRGL        V F +R+GEILGFAGL+GAGRTE+  
Sbjct: 240 RELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFE 299

Query: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377
            + G  P  AG + I G    +KSP DA  HG+ YLSEDRK  GL V   ++ N+ L ++
Sbjct: 300 GLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMAL 359

Query: 378 GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDIL 437
            R+ +  ++D  A + A +  V++  I+T S+E +A  LSGGNQQK+ +AK L     ++
Sbjct: 360 ERYAK-PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVV 418

Query: 438 FFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGEL 497
             DEPTRG+DVGAK EIY L+  LAEQG A+++ISSEL E++ + HRV VM  GR+   L
Sbjct: 419 VLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTL 478

Query: 498 ARADATQEKIMQLAT 512
                T+E+++  AT
Sbjct: 479 QEPHLTEEELIAHAT 493



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 65/235 (27%), Positives = 113/235 (48%), Gaps = 13/235 (5%)

Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPAD-- 344
           R +  V F L+ G + G  G  GAG++ + + + G +    GE+++ G    +++P    
Sbjct: 18  RVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGA---VRAPGGGS 74

Query: 345 --AVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQL 402
             A A GI  + ++   F LA  + +  NI L       R  F+D +A+RE  +  + ++
Sbjct: 75  RAAEAQGIVLIHQE---FNLADDLTIAQNIFLGH--EIKRGLFLDDKAMREKTREALAKV 129

Query: 403 AIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALA 462
            +     + + R L    +Q + IA+ L R+  +L  DEPT  +  G    ++ L+  L 
Sbjct: 130 GLPLDP-DTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALMAGLK 188

Query: 463 EQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESA 517
             G  I+ IS +L EV R +  V+VM +G +    A A  T+ ++  L   RE A
Sbjct: 189 AAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRELA 243



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 58/226 (25%), Positives = 108/226 (47%), Gaps = 9/226 (3%)

Query: 39  DNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALG 98
           +   FE+  GE+    G  GAG++ L + L G+  R +G + + G+PV++  PR A   G
Sbjct: 272 EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHG 331

Query: 99  IGIIHQELN---LMNHLSAAQNIFIGREPRKAMGLFID---EDELNRQAAAIFARMRLDM 152
           +  + ++     L  H     N+ +    R A   ++D   E    R+A   F      +
Sbjct: 332 LTYLSEDRKGKGLHVHFGLRPNLTLMALERYAKP-WLDPAAEQAALREAVQEFGIRTGSL 390

Query: 153 DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVG 212
           +       L+   QQ + +AK L     V+++DEPT  ++     E++ +++ L  QG+ 
Sbjct: 391 E--VRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLA 448

Query: 213 IVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           ++ IS ++ EL  +  RV+VMR G+   T+     + + +I+   G
Sbjct: 449 VIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATG 494


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: 638
Number of extensions: 35
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: 496
Length adjustment: 34
Effective length of query: 486
Effective length of database: 462
Effective search space:   224532
Effective search space used:   224532
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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