GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Acidovorax caeni R-24608

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_054255670.1 BN2503_RS05615 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= curated2:Q2G9T9
         (471 letters)



>NCBI__GCF_001298675.1:WP_054255670.1
          Length = 1335

 Score =  186 bits (473), Expect = 3e-51
 Identities = 140/430 (32%), Positives = 216/430 (50%), Gaps = 26/430 (6%)

Query: 17   VWRGKVGDVEEVVARARRAWPAWAAQPLATRIELVRRFANEVRKDADNLATMISRETGKP 76
            V+     DV+    RA +A P WA  P ATR + ++R A+ + + +  L  +I RE GK 
Sbjct: 685  VYEAAAHDVQAACERAAQAAPIWAGTPPATRADALQRAADLLEQRSQPLMGLIMREAGKT 744

Query: 77   LWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAALRHKPHGVLAVLGPYNFPAH 136
            L  A  E+   V+     +R Y  + + +  D+A Q       +P GV+  + P+NFP  
Sbjct: 745  LPNAVAEIREAVD----FLRYYGAQVATQ-FDNAAQ-------RPLGVVLAISPWNFPLA 792

Query: 137  LPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGIPAAVVQVLIG-GPEEGQALV 195
            +  G +  AL AGN V+ KP+E+TP T   +    H AG+P   +Q++ G G   G ALV
Sbjct: 793  IFCGQVAAALAAGNTVLAKPAEQTPLTAAAMVALLHEAGVPRDALQLVPGQGESVGAALV 852

Query: 196  AHDGIDGVLFTGSAHAGIAINRKLA---SNPGKIVAL--EMGGNNPIVVWDTPKIEDAAT 250
            AH  + GV+FTGS      I R+L+   S  G+ + L  E GG N +VV  +   E    
Sbjct: 853  AHPQVAGVMFTGSTEVARLIARQLSTRLSPTGQAIPLVAETGGQNAMVVDSSALAEQVVA 912

Query: 251  LIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGAPFDDPAPFMGPVIDN 310
             ++ SAF SAGQRC+A R L ++  + D  +  ++       +G P D     +GPVID 
Sbjct: 913  DVLASAFDSAGQRCSALRLLCLQDDVADRTLTMLRDALQEWTLGNP-DRLHTDVGPVID- 970

Query: 311  RTADGLTESFVYLLSSGGRPIKHMVRLQE--DRPFLSPAIIDVTAVADRPDVELFGPLLQ 368
              A    E+ +  ++  G+ +  + R     +  F++PAII++ + + R   E+FGP+L 
Sbjct: 971  AEARAQIEAHIARMADAGQTVTRVERTDGALNGHFVAPAIIEIDSTS-RLTREVFGPVLH 1029

Query: 369  VVRV--DDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVVNWNRPTNGA-SSA 425
            V+R   +  D  +   N T +GL+  +     +        I AG +  NR   GA    
Sbjct: 1030 VIRYPREQLDALLDGINATGYGLTFGVHSRIDETIQHLSERIHAGNLYVNRNVIGAVVGV 1089

Query: 426  APFGGVGLSG 435
             PFGG+GLSG
Sbjct: 1090 QPFGGMGLSG 1099


Lambda     K      H
   0.319    0.135    0.403 

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: 1435
Number of extensions: 72
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 471
Length of database: 1335
Length adjustment: 41
Effective length of query: 430
Effective length of database: 1294
Effective search space:   556420
Effective search space used:   556420
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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