GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Shewanella loihica PV-4

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 5208103 Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= curated2:Q87L22
         (485 letters)



>FitnessBrowser__PV4:5208103
          Length = 1059

 Score =  182 bits (462), Expect = 5e-50
 Identities = 151/469 (32%), Positives = 229/469 (48%), Gaps = 37/469 (7%)

Query: 4    WIAGEWVQGQ---GEEFVSLSPYNQ-EVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFA 59
            W AG  V G+   GE     SPY+  +++ +   A  + ++QA+A+A  AF  W   P  
Sbjct: 563  WSAGPIVNGETLSGETIEVKSPYDTTQIVGKVAFANNQAIEQALASAHNAFGSWCSTPVE 622

Query: 60   EREAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEA----------AAMAGKIAISI 109
             R   +   A+ ++EN E++  +  +E GK I +   E           A  A K+    
Sbjct: 623  VRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMGKP 682

Query: 110  RAYHDRTGEATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKP 169
                  TGE       N++ L+ R  GV     P+NFP  +  G +  AL AGNTVV KP
Sbjct: 683  ELLPGPTGEL------NELFLQGR--GVFVCISPWNFPLAIFLGQVTAALAAGNTVVAKP 734

Query: 170  SEQTPWTGELAMKLWEEAGLPKGVINLVQGAKET-GIALADAKGIDGILFTGSANTGHIL 228
            +EQT   G  A++L  EAG+PK  +  + G   T G  +   + I G+ FTGS  T   +
Sbjct: 735  AEQTSIVGYRAVQLAHEAGIPKEALQFLPGTGATVGATITADERIGGVCFTGSTVTAKRI 794

Query: 229  HRQFAGQPGKMLAL--EMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYV 286
            +   A + G ++ L  E GG N MV+ D+    +  V  ++ S+F SAGQRC+  R LY+
Sbjct: 795  NLTLAQRDGAIIPLIAETGGQNAMVV-DSTSQPEQVVNDVVSSSFTSAGQRCSALRVLYL 853

Query: 287  PFGEKGDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDAQANLQSLGGESL 346
               +  D +I  +  A   + +  P +     +GP I  A AK  L+A  +     G  +
Sbjct: 854  Q-EDIADRVIDVMKGAMDELTIGNPGSVKTD-VGPVID-ATAKANLNAHIDHIKQVGRLI 910

Query: 347  --IEAKAG--EAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLD--KAVELANDTRF 400
              +E  AG     FV+P  +++ +I  L ++E+FGP+L V+RY+  D  K ++  N T F
Sbjct: 911  NQLELPAGTENGHFVAPTAVEIDSIKVL-EKEHFGPILHVIRYKAADLPKVIDDINSTGF 969

Query: 401  GLSAGLVSTDDQEWEYFVDHIRAGIVNRNRQLTGA-SGDAPFGGPGASG 448
            GL+ G+ S ++       D +  G V  NR   GA  G  PFGG G SG
Sbjct: 970  GLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSG 1018


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: 1101
Number of extensions: 58
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: 1059
Length adjustment: 39
Effective length of query: 446
Effective length of database: 1020
Effective search space:   454920
Effective search space used:   454920
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