GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Caulobacter crescentus NA1000

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



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

 Score =  291 bits (745), Expect = 3e-83
 Identities = 173/473 (36%), Positives = 265/473 (56%), Gaps = 12/473 (2%)

Query: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP--AWRALTA 69
           QA IDG  V+A +G T    +P  G++L  V    A +  RA+  A  A     WR    
Sbjct: 22  QAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGP 81

Query: 70  KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYG 128
           +++   L R  EL+  + D+LA L +L+ GKP+++A+  +I  A +   W+AE   ++YG
Sbjct: 82  RQKKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYG 141

Query: 129 DVIPGHQPDKRL-IVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPF 187
           +V  G  P  RL   + +P+GV  AI PWNFP  M   K  PALA G ++VLKPA Q+P 
Sbjct: 142 EV--GTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPL 199

Query: 188 SAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK 247
           +A  L  LA  AG+P GV +V+ G  G  G  L  +  V  ++FTGS  +GR+LM   A+
Sbjct: 200 TALKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSAR 259

Query: 248 -DIKKVSLELGGNAPFIVFDDA-DLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAF 305
            ++K+VSLELGG +P IVF D  DL+ A + A    + N G+ C  A+RL ++  + DAF
Sbjct: 260 SNLKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAF 319

Query: 306 AEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPME--- 362
             ++      +K+G+ L+  T  G ++ E+ +    ++IA A S+GA  + GG+ +    
Sbjct: 320 LARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQEA 379

Query: 363 -GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDL 421
            G + EPTI   V  +  +A+EE FGP+  +  F  E + + ++NDT +GLA+  +  D+
Sbjct: 380 GGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADV 439

Query: 422 GRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
            +  R A  L+ G+V VN     +   PFGG K SG GR+ S + +  Y ++K
Sbjct: 440 SKALRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLK 492


Lambda     K      H
   0.317    0.135    0.390 

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: 558
Number of extensions: 32
Number of successful extensions: 7
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: 480
Length of database: 499
Length adjustment: 34
Effective length of query: 446
Effective length of database: 465
Effective search space:   207390
Effective search space used:   207390
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