Alignments for a candidate for araG in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Pseudomonas fluorescens FW300-N1B4

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243
          Length = 521

 Score =  233 bits (593), Expect = 2e-65
 Identities = 154/485 (31%), Positives = 247/485 (50%), Gaps = 19/485 (3%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P L  R I K +PG  A   I      G++HAL+GENGAGKSTL+KI+ G     +G ++
Sbjct: 12  PRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMI 71

Query: 66  INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125
             GQ ++  +   A   G+ +++Q   L   ++VA+NI L      G       L  +  
Sbjct: 72  WQGQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAG---TPKQLEPKIR 128

Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185
              +  GM ++P+  +  LSIG+ Q VEI + L ++ +++  DEPTS L+ +E D LF  
Sbjct: 129 EVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVT 188

Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245
           +R L  EG  IL++SH++ E+ AL  + TV + GR        Q  D   L Q MVG + 
Sbjct: 189 LRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQ-LAQLMVG-EA 246

Query: 246 GDIYGWQPRSYGEERLRLDAVKAPGVRTP---------ISLAVRSGEIVGLFGLVGAGRS 296
            ++    P+  G +     +V       P         I   VRSGEIVG+ G+ G G+ 
Sbjct: 247 AELITDYPKVMGADAFL--SVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGVAGNGQD 304

Query: 297 ELMKGMFGGTQIT---AGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRD 353
           EL+  + G  ++    +  +    QP+   +P      G+   P +R   G +P  S+ D
Sbjct: 305 ELLALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLAD 364

Query: 354 NINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRW 413
           N  ++A ++ ++   ++  G  +  A+  IR   +KTP +     +LSGGN QK ILGR 
Sbjct: 365 NALLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQKFILGRE 424

Query: 414 LSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMR 473
           + ++ K+++   PT G+DVGA   I+  + AL   G A+L  S DL E+  + DR+  + 
Sbjct: 425 ILQQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRLGALC 484

Query: 474 EGEIA 478
            G+++
Sbjct: 485 GGQLS 489



 Score = 87.8 bits (216), Expect = 8e-22
 Identities = 66/250 (26%), Positives = 124/250 (49%), Gaps = 20/250 (8%)

Query: 260 RLRLDAVKAPG--VRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQ 317
           +LR  + + PG      I L++  GEI  L G  GAG+S LMK ++G T   +G++    
Sbjct: 15  QLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQG 74

Query: 318 QPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVH-SVRDNINISARRKHVLGGCVINNGWEE 376
           Q + +R P+ A   G+          G++  H S+ + ++++      +G          
Sbjct: 75  QRVTMRNPAQARGLGI----------GMVFQHFSLFETLSVAQNIALAMGAAA----GTP 120

Query: 377 NNADHHIRSLNIKTPGA---EQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVG 433
              +  IR ++ +   A   E+L+ +LS G +Q+  + R L +++++++LDEPT  +   
Sbjct: 121 KQLEPKIREVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQ 180

Query: 434 AKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALS 493
              E++  +  LAA+G ++LF S  L EV  +     V+R G +AG  +  Q  +RQ   
Sbjct: 181 EADELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQ 240

Query: 494 LAMPKVSQAV 503
           L + + ++ +
Sbjct: 241 LMVGEAAELI 250


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: 637
Number of extensions: 36
Number of successful extensions: 8
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: 521
Length adjustment: 35
Effective length of query: 469
Effective length of database: 486
Effective search space:   227934
Effective search space used:   227934
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.

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Protein sequences (fasta format)
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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