GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Caulo:CCNA_03243 CCNA_03243 NADP+-dependent
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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