Alignments for a candidate for BPHYT_RS16930 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Acidovorax sp. GW101-3H11

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  330 bits (846), Expect = 7e-95
 Identities = 189/488 (38%), Positives = 299/488 (61%), Gaps = 20/488 (4%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L+   I K F G+  L  V  ++  G++H LMG+NGAGKSTL+K+L G  +   G++ + 
Sbjct: 19  LQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLG 78

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS-------LGWVNKREA 117
           G  V   S  ++   GI+ ++QE+   P+L+VAEN+  G+ P         + W    + 
Sbjct: 79  GQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQR 138

Query: 118 KRFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETE 177
            R +  R+   G+ +D    L    +A +Q+V I +AL   +RV+ LDEPTSSL   E +
Sbjct: 139 ARDLVARI---GLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195

Query: 178 VLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEM 237
            LF+++R LR++  ++++++H ++++Y + D  T+ R+G  +      + +    +++ M
Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEW-LAKDLGPQALIAAM 254

Query: 238 VGREISDIYNYSA-RPLGEVRFA----AKGIEGHALAQPASFEVRRGEIVGFFGLVGAGR 292
           +GR+++      A  P  + R A    A+G+      QP   ++R GE+VG  GL+G+GR
Sbjct: 255 LGRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGR 314

Query: 293 SELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENI 352
           +EL  L++G +    G L +DG+ +K  +  +AIRHG+ LCPE+RK +GIVA  +V ENI
Sbjct: 315 TELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENI 374

Query: 353 NISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLA 412
            ++ +   + VG FL R ++ E A+R++KLL IKT +  + I  LSGGNQQKAIL+RW+A
Sbjct: 375 ALALQAR-MGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMA 433

Query: 413 -EPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMR 471
            EP  +++ILDEPTRGIDV AK EI + I +LA+ G A++ ISSE+ EV+ V+ RIVV+R
Sbjct: 434 IEP--RLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLR 491

Query: 472 QGRISGEL 479
             R  GEL
Sbjct: 492 DRRKVGEL 499



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 59/225 (26%), Positives = 108/225 (48%), Gaps = 8/225 (3%)

Query: 20  LDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVRFTSAASSIAA 79
           L  +   +  G+V GL G  G+G++ L ++L G  QPD G + IDG  V+F +   +I  
Sbjct: 291 LQPLDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRH 350

Query: 80  GIAVIHQELQ---YVPDLTVAENLLLG-QLPNSLG-WVNKREAKRFVRERLEAMGVALDP 134
           G+A+  +E +    V +L+V EN+ L  Q    +G ++++ E        ++ +G+  + 
Sbjct: 351 GLALCPEERKTDGIVAELSVRENIALALQARMGVGKFLSRSEQTELAERYVKLLGIKTET 410

Query: 135 NAK-LRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRADNRAM 193
             K +  LS   +Q   + + +    R++ LDEPT  +     + +   +  L     A+
Sbjct: 411 VDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAV 470

Query: 194 IYISHRMDEIYELCDACTIFRDGRKIASHP--TLEGVTRDTIVSE 236
           ++IS  M E+  +     + RD RK+   P  + E    D I +E
Sbjct: 471 LFISSEMSEVVRVAHRIVVLRDRRKVGELPAGSSEDAVYDLIAAE 515



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 74/274 (27%), Positives = 124/274 (45%), Gaps = 10/274 (3%)

Query: 238 VGREISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMH 297
           V  + S  +  +A P+ ++    K   G  + +     +  GEI    G  GAG+S L+ 
Sbjct: 3   VSMDASTAHAPAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIK 62

Query: 298 LVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCR 357
           ++ G     GG++ L G+ +   S   A R GI    +   E  +    +V+ENI     
Sbjct: 63  VLTGVLEASGGQMRLGGQAVWPDSPLAAQRLGISTVYQ---EVNLCPNLSVAENIFAG-- 117

Query: 358 RHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSG---GNQQKAILSRWLAEP 414
             Y R G+    + +  T  +  + L  +   +    R LS      QQ   ++R L+  
Sbjct: 118 -RYPRCGIAQGFRIDWATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSI- 175

Query: 415 DLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGR 474
           + +V+ILDEPT  +D     +++ V+ +L   G +IV ++  L +V  VSDRI V+R G 
Sbjct: 176 ESRVLILDEPTSSLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGS 235

Query: 475 ISGELTRKDATEQSVLSLALPQSSTALPGTQAAA 508
             GE   KD   Q++++  L +   A     A A
Sbjct: 236 WVGEWLAKDLGPQALIAAMLGRDLAAASEQPAPA 269


Lambda     K      H
   0.320    0.136    0.385 

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: 26
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: 512
Length of database: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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