GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PV4:5208103 Shew_0615 bifunctional proline
            dehydrogenase/pyrroline-5-carboxylate dehydrogenase
            (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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