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_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  366 bits (940), Expect = e-105
 Identities = 199/503 (39%), Positives = 320/503 (63%), Gaps = 7/503 (1%)

Query: 14  ASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ 73
           A + ++ PV+ L  + K+F G+  L + Q  L  GE+HALMG+NGAGKSTL+K+L+GV +
Sbjct: 10  AHAPAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLE 69

Query: 74  RDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRK--AMGLF 131
              G + L G+ V    P  AQ LGI  ++QE+NL  +LS A+NIF GR PR   A G  
Sbjct: 70  ASGGQMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFR 129

Query: 132 IDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAAL 191
           ID   L+++A  + AR+ L +D +  + +  VA QQ+V IA+ALS +SRVLI+DEPT++L
Sbjct: 130 IDWATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSL 189

Query: 192 NNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDT 251
           ++ E+ +LF ++R L+++G+ IV+++H ++++  ++DR++V+R+G ++     ++     
Sbjct: 190 DDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQA 249

Query: 252 IISMMVGR--ALDGEQRIPPDT--SRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGL 307
           +I+ M+GR  A   EQ  P     SR+  +L+  GL +   ++ +   +R GE++G AGL
Sbjct: 250 LIAAMLGRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGL 309

Query: 308 MGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367
           +G+GRTE+AR +FG +  + G + I G      +P DA+ HG+    E+RK  G+   + 
Sbjct: 310 LGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELS 369

Query: 368 VQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIA 427
           V+ NIAL+   R     F+ +    E A+ YV+ L IKT +V++   LLSGGNQQK ++A
Sbjct: 370 VRENIALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILA 429

Query: 428 KWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLV 487
           +W+  +  +L  DEPTRGIDV AK EI   +  LA+ G A++ ISSE+ EV+R++HR++V
Sbjct: 430 RWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVV 489

Query: 488 MCEGRITGELARADATQEKIMQL 510
           + + R  GEL  A ++++ +  L
Sbjct: 490 LRDRRKVGELP-AGSSEDAVYDL 511



 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 67/256 (26%), Positives = 116/256 (45%), Gaps = 22/256 (8%)

Query: 277 VLEVRGLNRGRA----IRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           VL++ G+++  A    +RDV   L  GEI    G  GAG++ + + + G      G++ +
Sbjct: 18  VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGF-----MD 387
            G      SP  A   GI  + ++     L   + V  NI     GR+ R G      +D
Sbjct: 78  GGQAVWPDSPLAAQRLGISTVYQE---VNLCPNLSVAENIFA---GRYPRCGIAQGFRID 131

Query: 388 QRAIREAAQMYVRQLAIKTPSVEQQARLLSG---GNQQKIVIAKWLLRDCDILFFDEPTR 444
              + + A+  V ++ ++        RLLS      QQ + IA+ L  +  +L  DEPT 
Sbjct: 132 WATLHQRARDLVARIGLQI----DVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTS 187

Query: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504
            +D     +++++L  L  +G +IV ++  L +V  +S R+ V+  G   GE    D   
Sbjct: 188 SLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGP 247

Query: 505 EKIMQLATQRESAVAS 520
           + ++     R+ A AS
Sbjct: 248 QALIAAMLGRDLAAAS 263


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: 618
Number of extensions: 27
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: 520
Length of database: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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