Alignments for a candidate for BPHYT_RS16930 in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Caulobacter crescentus NA1000

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  377 bits (969), Expect = e-109
 Identities = 220/499 (44%), Positives = 314/499 (62%), Gaps = 10/499 (2%)

Query: 21  IGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTMA 80
           + KSFPGV+AL  +  V   G+VHAL+GENGAGKSTL+KIL  A+   +G +    Q + 
Sbjct: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68

Query: 81  FKGTADSIAS-GVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTLLKGL 139
            +         G+A I+QE +L PE++VAEN++LG  P R GLV+   LR  A  LL  L
Sbjct: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128

Query: 140 ADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRD 199
              ++P   V  L++ ++Q+VEIAKA++  A +I  DEPT++LS RE+DRL AII  L+ 
Sbjct: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188

Query: 200 EGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQDIYDY 259
               V+YVSHR+ EV  +C+  TV +DGR+V + + ++++    +V  MVGR ++     
Sbjct: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGD-VADVEVADMVRLMVGRHVEFERRK 247

Query: 260 RPRERGDVALQVKG-------LLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSG 312
           R R  G V L+V+G       L  PG    VSF    GEI+GL GLVGAGRT+L RL+ G
Sbjct: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307

Query: 313 LERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHS 372
            +    G +++ DK L+LRSPRDAI AG++L PEDRK++G     S+  N+++ +  + S
Sbjct: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367

Query: 373 TLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432
            LG  +    ER   +   + L++K   A   I  LSGGNQQK +LGR +++  KVL++D
Sbjct: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427

Query: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492
           EPTRGIDIGAKAE++Q++ +LA  G+AV+V+SS+L EVM +SDRI+V  EG +  +L   
Sbjct: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487

Query: 493 QANESNLL-QLALPRQRVA 510
            A E  L+  +A    RVA
Sbjct: 488 TATEEGLMAYMATGTDRVA 506



 Score = 65.1 bits (157), Expect = 6e-15
 Identities = 60/220 (27%), Positives = 99/220 (45%), Gaps = 10/220 (4%)

Query: 266 DVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHD 325
           DV+   K   G    + V   V  GE+  L G  GAG++ L+++LS       G++    
Sbjct: 5   DVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAG 64

Query: 326 KELKLRSPRDA-IAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWER 384
           + L    PRDA +    L      ++  + P  SV EN+ +   P    LG +   DW R
Sbjct: 65  QVL---DPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR--LGLV---DWSR 116

Query: 385 GNADKQIKSLKVKTP-TAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAK 443
             AD Q     +  P      +  L+   QQ   + + +++  +++++DEPT  +     
Sbjct: 117 LRADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREV 176

Query: 444 AEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEG 483
             ++ II  L A  ++VI VS  L EV  + DR  V+ +G
Sbjct: 177 DRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDG 216


Lambda     K      H
   0.320    0.138    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: 736
Number of extensions: 41
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: 514
Length of database: 515
Length adjustment: 35
Effective length of query: 479
Effective length of database: 480
Effective search space:   229920
Effective search space used:   229920
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.

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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