GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03243
          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 (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