GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Caulobacter crescentus NA1000

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= curated2:Q1QTQ7
         (489 letters)



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

 Score =  211 bits (537), Expect = 5e-59
 Identities = 164/467 (35%), Positives = 228/467 (48%), Gaps = 15/467 (3%)

Query: 6   QLLIDGAWVDG-DAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPD--WARRSF 62
           Q +IDG  V+    A F    P  G+ L   TA  A  VE AVA AR AF D  W  +  
Sbjct: 22  QAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGP 81

Query: 63  AERQAVVERFRECLETHREHLATAIAQETGKPLWEART-EVGAMIGKVAISITAYHERTG 121
            +++AV+ R  E +E   + LA   + + GKP+ +AR  ++   I        A  +  G
Sbjct: 82  RQKKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYG 141

Query: 122 ERARDIGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTA 181
           E      D  +   H P GV+    P+NFP H+    + PAL  GN+VV KP+EQ+P+TA
Sbjct: 142 EVGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTA 201

Query: 182 DLTLQCWLEAGLPAGVINLVQGAAEV-GQALAGSADIDGLLFTGSAKVGGLLHRQFGGQV 240
                  LEAGLP GV+N++ G   V G+ALA S D+D + FTGS  VG  L        
Sbjct: 202 LKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSN 261

Query: 241 DKILALELGGNNP-LVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLI 299
            K ++LELGG +P +V  D PD EAA  +     F + G+ CT A RL+V    + D  +
Sbjct: 262 LKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLV-EAPIKDAFL 320

Query: 300 DALTSAIAELRVAAPFSEPAPFYAGLT--SVEAADGLLAAQDDLVARGGRPLSRMR-RLQ 356
             +      ++V  P      F A ++   +  A   +A  D   AR  R L   R R +
Sbjct: 321 ARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGAR--RVLGGQRVRQE 378

Query: 357 AGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGE 414
           AG   + P + D    D  +  EE FGP+L V  +   DEA+ LANDT YGL+AGL   +
Sbjct: 379 AGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTAD 438

Query: 415 RADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYA 461
            +       R++AG+V W           PFGG   SG  R  + +A
Sbjct: 439 VSKALRGARRLKAGLV-WVNGWDACDITMPFGGFKQSGFGRDRSLHA 484


Lambda     K      H
   0.319    0.135    0.409 

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: 598
Number of extensions: 40
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 489
Length of database: 499
Length adjustment: 34
Effective length of query: 455
Effective length of database: 465
Effective search space:   211575
Effective search space used:   211575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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