GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Caulobacter crescentus NA1000

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Caulo:CCNA_03243
          Length = 499

 Score =  357 bits (915), Expect = e-103
 Identities = 190/475 (40%), Positives = 284/475 (59%), Gaps = 4/475 (0%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL-NGPWKKMTANER 73
           IDG  V +  G TF N++P   + L  V    A +++ AV  A+ A  +G W+     ++
Sbjct: 25  IDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQK 84

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133
            AVL ++ +L+    +EL++LESLD GKP   + ++DIP A     ++++ +  +  E  
Sbjct: 85  KAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYGEVG 144

Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193
                 L+YA+  P+GVIG I PWN PL +  WK+APALA GN+VV+KPAE +P+TA  L
Sbjct: 145 TSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTALKL 204

Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA-SAAKTLK 252
             +  +AG+P GV+N++ G G   AG AL    DV+ I+FTG    G+ +M  SA   LK
Sbjct: 205 GALALEAGLPPGVLNVIPGLG-GVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNLK 263

Query: 253 RLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311
           R+S ELGGK+P ++FAD  +L+   +      F NQGEVC   SR+ VE P  +AFL + 
Sbjct: 264 RVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLARV 323

Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371
           +   K + VGDP D  T+ GA++S+        YI  A  +G   + GG+R      G++
Sbjct: 324 IEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQEAGGFY 383

Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431
           +EPTI   +  D  + +EE+FGPV+ V+ F +E+E +   NDT YGL+A +WT D+ +A 
Sbjct: 384 VEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADVSKAL 443

Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
           R A +++AG+VWVN W   D+  PFGG KQSG GR+  LH+   Y++L ++ + L
Sbjct: 444 RGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLKSVSVTL 498


Lambda     K      H
   0.318    0.136    0.404 

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: 564
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 486
Length of database: 499
Length adjustment: 34
Effective length of query: 452
Effective length of database: 465
Effective search space:   210180
Effective search space used:   210180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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.

Links

Downloads

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:

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:

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:

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:

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