GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Shewanella amazonensis SB2B

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__SB2B:6938534
          Length = 480

 Score =  216 bits (549), Expect = 2e-60
 Identities = 155/475 (32%), Positives = 225/475 (47%), Gaps = 25/475 (5%)

Query: 41  YIGGEWVD--TKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98
           YI GEW D  + E +   NP A +E + +    G+ E   A+ AA  A   W+    ++R
Sbjct: 14  YINGEWRDALSGETVTIANP-ATNEAIASVPVMGRDETREAIAAAEAALPAWRALTAKER 72

Query: 99  SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158
              L +   LM     +L   +  E GK   EA  +V  A  FIE++A  A R      +
Sbjct: 73  GAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAEEAKRLYG---D 129

Query: 159 VVPYPGEDNESFYVPLGAGVV--IAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216
            +P    D     +  G GV   I PWNFP A+ T      +A G T+I KPA       
Sbjct: 130 TIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTA 189

Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276
             + E+  EAG PPGV + + G    +G  L E+P  R ++FTGS  VG+K+ +   + A
Sbjct: 190 LALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQ---QCA 246

Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336
           P     K+  +E GG    IV   AD D A EG ++S Y   GQ C  A+RL +  G Y+
Sbjct: 247 P---TLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYD 303

Query: 337 PVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEG 394
              +++     +L VG  AE     GP+++A    KV S+++   ++G  LV GGK L G
Sbjct: 304 AFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPLGG 363

Query: 395 EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKR 454
              F+ P + T V    ++A+EE FGP+  + R  D  + +  ANDT +GL    Y R  
Sbjct: 364 N--FMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDI 421

Query: 455 EHLEWARREFHVGNLYFNRKITGAL-VGVQPFGGFKLSG---TNAKTGALDYLRL 505
             +         G +  N   TG +   V PFGG K SG     +K G  +Y+ +
Sbjct: 422 SLIWKVAEALEYGMVGVN---TGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEI 473


Lambda     K      H
   0.319    0.137    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: 575
Number of extensions: 28
Number of successful extensions: 4
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: 516
Length of database: 480
Length adjustment: 34
Effective length of query: 482
Effective length of database: 446
Effective search space:   214972
Effective search space used:   214972
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: 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