GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03243
          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 (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