GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Caulobacter crescentus NA1000

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03243 CCNA_03243 NADP+-dependent
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          Length = 499

 Score =  295 bits (756), Expect = 2e-84
 Identities = 178/474 (37%), Positives = 263/474 (55%), Gaps = 8/474 (1%)

Query: 6   LINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKV 62
           +I+G+LV +  G      +P  G VL  +    A+ V+ AV  A AAF +  W    P+ 
Sbjct: 24  VIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQ 83

Query: 63  RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122
           +   L +LA+++E +    A LES + GKP+  A N +IP  ++  R++A A   + G  
Sbjct: 84  KKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYG-E 142

Query: 123 AGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTAL 182
            G       S    +PLGV+ +I PWN+PL MA WK+APALA GN VVLKP+E +PLTAL
Sbjct: 143 VGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202

Query: 183 KLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTA-SSI 240
           KL  LA +   P GV+N++ G G   G+ L     V M++ TGS   G  ++ ++A S++
Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNL 262

Query: 241 KRTHMELGGKAPVIVFDDA-DIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK 299
           KR  +ELGGK+P IVF D  D+EA  +      +YN G+ CTAA R+  +  I D  + +
Sbjct: 263 KRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLAR 322

Query: 300 LGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-GNGY 358
           +      +K G P D ST+ G + S   +      +  A + G  +V+ G   R+   G+
Sbjct: 323 VIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQEAGGF 382

Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418
           Y  PT+      D  + ++EVFGPV+ V  F +E++ +  AND+ YGLA+ +WT DV +A
Sbjct: 383 YVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADVSKA 442

Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472
            R + RL+ G  WVN        MP GG K SG+G+D SL+ L  Y  ++ V V
Sbjct: 443 LRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLKSVSV 496


Lambda     K      H
   0.317    0.134    0.397 

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: 505
Number of extensions: 21
Number of successful extensions: 6
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: 474
Length of database: 499
Length adjustment: 34
Effective length of query: 440
Effective length of database: 465
Effective search space:   204600
Effective search space used:   204600
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