GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Dyella japonica UNC79MFTsu3.2

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Query= curated2:Q87L22
         (485 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4232
          Length = 1074

 Score =  185 bits (469), Expect = 8e-51
 Identities = 150/440 (34%), Positives = 218/440 (49%), Gaps = 24/440 (5%)

Query: 25   QEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAEREAIVLAFAEKVKENSEKIAEVIA 84
            ++V+     A +  V++A+A A AA   W + P A R AI+   AE+++    +   +  
Sbjct: 605  RQVVGSYVSADSATVEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFIALCV 664

Query: 85   KETGK----PIWETRTEAAAMAGKIAISIRAYHDRTGEATREAA-GNQIVLRHRPLGVMA 139
            +E GK     I E R EAA      A   R Y  +  +        NQ+ L  R  GV  
Sbjct: 665  REAGKGLPDAIAEIR-EAADFLRYYATMARRYFGQPEQLPGPTGESNQLFLNGR--GVFV 721

Query: 140  VFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTGELAMKLWEEAGLPKGVINLVQG 199
               P+NFP  +  G +  AL AGN+V+ KP+EQT   G  A++L  EAG+P  V+  + G
Sbjct: 722  CISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHEAGVPADVLQYLPG 781

Query: 200  AKET-GIALADAKGIDGILFTGSANTGHILHRQFAGQPGKMLAL--EMGGNNPMVISDNY 256
               T G AL     + G+ FTGS  T   ++R  A +   + AL  E GG N M I+D+ 
Sbjct: 782  DGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAALIAETGGQNAM-IADSS 840

Query: 257  GDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALITKLVEATKNIRMDQPFAEPA 316
               +  V   + SAF SAGQRC+ AR LYV   +  D +   L  A   +++  P A+ +
Sbjct: 841  ALPEQIVKDAVSSAFQSAGQRCSAARVLYVQ-EDIADKVCAMLAGAMAELKVGDP-AQLS 898

Query: 317  PFMGPQISVAAAKFILDAQANL----QSLGGESLIEAKAGEAAFVSPGIIDVTNIAELPD 372
              +GP I   A K ++D  A +    + +G  +L  A  G   F +P   ++  +A L  
Sbjct: 899  TDVGPVIDEDARKILVDHAARMDQEAKKIGEVALDPATTGNGTFFAPRAYEIPGLATL-T 957

Query: 373  EEYFGPLLQVVRYEG--LDKAVELANDTRFGLSAGLVSTDDQEWEYFVDHIRAG--IVNR 428
             E FGP+L V+R++G  LDK V+  N T +GL+ G+ S  D   E+     R G   VNR
Sbjct: 958  REIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQSRARVGNCYVNR 1017

Query: 429  NRQLTGASGDAPFGGPGASG 448
            N Q+    G  PFGG G SG
Sbjct: 1018 N-QIGAVVGVQPFGGEGLSG 1036


Lambda     K      H
   0.316    0.134    0.397 

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: 1181
Number of extensions: 56
Number of successful extensions: 6
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: 485
Length of database: 1074
Length adjustment: 40
Effective length of query: 445
Effective length of database: 1034
Effective search space:   460130
Effective search space used:   460130
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 (21.6 bits)
S2: 55 (25.8 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