Alignments for a candidate for araG in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Caulobacter crescentus NA1000

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  377 bits (968), Expect = e-109
 Identities = 213/484 (44%), Positives = 306/484 (63%), Gaps = 9/484 (1%)

Query: 13  IGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMS 72
           + K+FPGV+AL  +      G+VHAL+GENGAGKSTL+KILS  +A   G+V   GQ + 
Sbjct: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68

Query: 73  FSDTTAALNA-GVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQLKHL 131
             D        G+A IYQE +L PE++VAEN+YLG+ P + G+V+ S L  +A   L  L
Sbjct: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128

Query: 132 GMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRK 191
           G+ ++PD P++ L++ + QMVEIAKA+  NA++I  DEPT++LS RE+D L  +I  L+ 
Sbjct: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188

Query: 192 EGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGDIYGW 251
               ++YVSHR+ E+ A+ D  TV +DGR+V +  D+  V+   +V+ MVGR +      
Sbjct: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFERRK 247

Query: 252 QPRSYGEERLRLDAV-------KAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304
           + R  G   L+++ V        APG    +S A R GEIVGL GLVGAGR++L + +FG
Sbjct: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307

Query: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364
              I AG+V +D +P+ +R P  AI AG+ML PEDRK +G    HS+R N+++ + +   
Sbjct: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367

Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424
             G  ++   E +  + + + L IK   AE  I  LSGGNQQK +LGR ++   KV+++D
Sbjct: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427

Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484
           EPTRGID+GAK E++ V+  LA  GVAV+  SS+L EV+ V+DRIVV REG I  +L  +
Sbjct: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487

Query: 485 QADE 488
            A E
Sbjct: 488 TATE 491



 Score = 71.6 bits (174), Expect = 6e-17
 Identities = 59/247 (23%), Positives = 110/247 (44%), Gaps = 19/247 (7%)

Query: 8   LSFRGIGKTFPGVKA---LTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64
           L   G+    P + A   L  +SF    G++  L G  GAG++ L +++ G      G V
Sbjct: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKGGI------- 114
           +++ + +       A+ AG+ ++ ++        + ++  N+ L  L     +       
Sbjct: 317 LVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDER 376

Query: 115 VNRSLLN-YEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSS 173
             R L+  Y   L++K      D +T +  LS G  Q V + +A+A   K++  DEPT  
Sbjct: 377 AERDLVETYRQKLRIKMA----DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432

Query: 174 LSAREIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDH 233
           +       + +V+ +L   G  ++ +S  + E+ A+SD I VF++G  V    D Q    
Sbjct: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL-DAQTATE 491

Query: 234 DALVQAM 240
           + L+  M
Sbjct: 492 EGLMAYM 498


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: 729
Number of extensions: 38
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: 504
Length of database: 515
Length adjustment: 34
Effective length of query: 470
Effective length of database: 481
Effective search space:   226070
Effective search space used:   226070
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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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