Alignments for a candidate for HSERO_RS03640 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Acidovorax sp. GW101-3H11

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_1109 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1109
          Length = 513

 Score =  280 bits (717), Expect = 7e-80
 Identities = 174/491 (35%), Positives = 271/491 (55%), Gaps = 19/491 (3%)

Query: 11  GIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPV 70
           GI K + A +A S + LT+ PGEIHA++GENGAGKSTLMK++ G   PD+G +  +G+ V
Sbjct: 2   GITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAV 61

Query: 71  ALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQ 130
            +R+P  +RA GI +++Q  ++   ++VA NV++G +    L     A +  R  A   +
Sbjct: 62  QVRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLDKSLTL-----AEVTQRISAKAAE 116

Query: 131 LGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLR 190
            G           LS+ E Q+VEI RAL+   +++I+DEPT+ L+ +  E+LF V+R+L 
Sbjct: 117 YGLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLA 176

Query: 191 DEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQH 250
            EG +I+YISH++ E+ AL    TVLR G   G     E  +  + ++M+G       +H
Sbjct: 177 SEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPPAL-EH 235

Query: 251 QRIAPADAAQLPTVMQVRALA-------GGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           + +         TV++V+ L+       G  +    F+V+AGEV+G AG+ G G+ EL  
Sbjct: 236 RAVQTG-----ATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLY 290

Query: 304 LLFGADPRSG-GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362
            L G D R+    I + G+      P      G+ +VPE+R G+G    M +A N  +  
Sbjct: 291 ALSGEDQRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTR 350

Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
            +     G ++  +L   A   IQR NVK   P +    LSGGN QK ++ R ++  PK+
Sbjct: 351 KNAVGGSGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKL 410

Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482
           LI+ +PT GVD+ A ++I   +  L   G AV+V+S EL E+  ICDR+ V+ +G ++  
Sbjct: 411 LIVSQPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPS 470

Query: 483 LAGAAITQENI 493
           +  A  T E I
Sbjct: 471 VQRAEATVERI 481



 Score = 97.4 bits (241), Expect = 1e-24
 Identities = 73/231 (31%), Positives = 112/231 (48%), Gaps = 22/231 (9%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           S  V  GE+    G  GAG++ L ++++G+     G +   G+ V +  P+ A   GIA 
Sbjct: 17  SLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAVQVRNPQEARALGIAM 76

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAH---- 394
           V +      LF  + VA N           LGL +S +L  V     QR++ K A     
Sbjct: 77  VFQHFS---LFDTLTVAENVW---------LGLDKSLTLAEVT----QRISAKAAEYGLD 120

Query: 395 --PETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGV 452
             P  PV  LS G  Q+V + R L   PKVLILDEPT  +   A  +++ ++ +LAS+G 
Sbjct: 121 IDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLASEGC 180

Query: 453 AVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVP 503
           +++ IS +L E+  +C    V+R G +TG    +  T  ++ RL      P
Sbjct: 181 SILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPP 231



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 58/250 (23%), Positives = 113/250 (45%), Gaps = 12/250 (4%)

Query: 2   TQTPLLQMRGIR----KSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV-H 56
           T   +L+++G+       FG  L   D+   ++ GE+  + G +G G+  L+  LSG   
Sbjct: 240 TGATVLRVKGLSLPRADQFGVDLI--DLQFEVKAGEVVGIAGVSGNGQKELLYALSGEDQ 297

Query: 57  APDQGEILLDGRPVALRDPGASRAAGINLIYQEL---AVAPNISVAANVFMGSELRTR-L 112
             +   I + G+      PG  RA G++ + +E       P + +A N+ +  +      
Sbjct: 298 RAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAVGGS 357

Query: 113 GLIDHAAMRSRTDAVLRQLGAGFGASDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPT 171
           G I   A++   + ++++     G    A + LS    Q+  + R +    +++I+ +PT
Sbjct: 358 GWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVSQPT 417

Query: 172 AALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEID 231
             +      Q+   +  LRD G A++ +S  + E++ + DR+ V+  G     + R E  
Sbjct: 418 WGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRAEAT 477

Query: 232 SERIVQMMVG 241
            ERI + M G
Sbjct: 478 VERIGEWMSG 487


Lambda     K      H
   0.320    0.135    0.378 

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: 618
Number of extensions: 44
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: 521
Length of database: 513
Length adjustment: 35
Effective length of query: 486
Effective length of database: 478
Effective search space:   232308
Effective search space used:   232308
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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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