Alignments for a candidate for araG in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Pseudomonas fluorescens GW456-L13

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  335 bits (858), Expect = 3e-96
 Identities = 192/473 (40%), Positives = 277/473 (58%), Gaps = 6/473 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           LS  GIGKT+     L  I      G+V AL GENGAGKSTL KI+ G   PTTG +   
Sbjct: 10  LSVSGIGKTY-AQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQ 68

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           GQ+        A   G+ ++ QEL+L+P ++VAEN++L  LP KGG ++R  L   A   
Sbjct: 69  GQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAIEA 128

Query: 128 LKHLGMD-IDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
           + H+G+D IDPDT +  L IG  QMVEIA+ L  +  ++  DEPT+ L+ARE++ LF  I
Sbjct: 129 MAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQI 188

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246
             L+  G  I+Y+SHR+EE+  ++  I V +DG  V     M   + + LV  MVGR++G
Sbjct: 189 TRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLV-CVEPMANYNSEQLVTLMVGRELG 247

Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306
           +      R  G   L ++ +        +S  VR+GEI G+ GL+GAGR+EL++ +FG  
Sbjct: 248 EHIDMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGAD 307

Query: 307 QITAGQVYIDQ--QPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364
              +G + +    Q I++R P  A+  G+ L  EDRK EG++   S+  NI +      +
Sbjct: 308 IADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALG-NMPGI 366

Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424
            G   ++N  E   A   I ++ I++ G  QL+  LSGGNQQK ++GRWL  +  V+L D
Sbjct: 367 SGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFD 426

Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEI 477
           EPTRGIDVGAK +IYN++  L  QG A++  SSDL E++ + DRI V+  G +
Sbjct: 427 EPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSL 479



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 60/248 (24%), Positives = 115/248 (46%), Gaps = 18/248 (7%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P L+  G+ ++      + D+SF+  AG++  + G  GAG++ LL+++ G     +G++ 
Sbjct: 260 PVLTVNGLSRS----DKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIA 315

Query: 66  ING--QEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSLL 120
           +    Q ++      A+  G+A+I ++     L+   ++  NI LG +P   GI     +
Sbjct: 316 LGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGNMP---GISGAGFV 372

Query: 121 NYEAGLQLKHLGMDI------DPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSL 174
           + +    L    +D        P   +  LS G  Q V I + L R+  ++ FDEPT  +
Sbjct: 373 DNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDEPTRGI 432

Query: 175 SAREIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHD 234
                 +++ ++ EL ++G+ ++ VS  + E+  + D I V   G  + TF        +
Sbjct: 433 DVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDSWTQDE 492

Query: 235 ALVQAMVG 242
            L  A  G
Sbjct: 493 LLAAAFAG 500


Lambda     K      H
   0.319    0.136    0.391 

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: 655
Number of extensions: 30
Number of successful extensions: 10
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: 504
Length of database: 517
Length adjustment: 35
Effective length of query: 469
Effective length of database: 482
Effective search space:   226058
Effective search space used:   226058
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 (21.7 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, or view the source code.

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