GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Klebsiella michiganensis M5al

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase

Query= curated2:Q2SXN9
         (487 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS05620 BWI76_RS05620 NAD-dependent
           succinate-semialdehyde dehydrogenase
          Length = 482

 Score =  212 bits (540), Expect = 2e-59
 Identities = 153/463 (33%), Positives = 227/463 (49%), Gaps = 8/463 (1%)

Query: 3   ELFIDGAWVDGAGP-VFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDA 61
           +  I+G W D +G    A  NP   + +       A +   A+ +A RA  AW AL    
Sbjct: 12  QAMINGRWRDASGKETLAVTNPANGQPLGNVPKMGAGETREAIDAAARALPAWRALTAKE 71

Query: 62  RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK- 120
           R +I++R+  L++E ++ LA ++  E GKPL EA+ E++  A+ ++          G+  
Sbjct: 72  RSSILRRWFELMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTI 131

Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180
               AD   ++  +P GV A   P+NFP  +      PAL AG T+V KP+   P  A A
Sbjct: 132 PGHQADKRLLVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPFSALA 191

Query: 181 TVEIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239
             E+   AG+P GV N+V G   + G  L  +  +  L FTGS++ G  L +Q     + 
Sbjct: 192 LAELANRAGIPEGVFNVVTGSASEVGGELTGNPLVRKLSFTGSTEIGRQLMEQCAKDIKK 251

Query: 240 VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARL 299
           V +LE+GGN P +V +  D+D AV  A+ S F +AGQ C CA R+ V    + DRF  +L
Sbjct: 252 V-SLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDSVY-DRFAEKL 309

Query: 300 ADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALGFV 359
               SK+        P   +G +I  +A +++    A  +G GA  +   K  +    F 
Sbjct: 310 QQAVSKLQIG-DGLQPNVTIGPLIDEKAIAKVQEHIADALGKGARVVTGGKAHELGGNFF 368

Query: 360 NAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHT 418
              IL DV    ++  EE FGPLA + R+ D  D IA+ANDT FGL+A   A D      
Sbjct: 369 QPTILVDVPGDAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLGRVFR 428

Query: 419 FRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461
              A+  GI+  N     ++  APFGG   SG  R  + Y  +
Sbjct: 429 VGEALEYGIIGINTGLI-STEVAPFGGVKSSGLGREGSKYGIE 470


Lambda     K      H
   0.320    0.134    0.402 

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: 498
Number of extensions: 24
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: 487
Length of database: 482
Length adjustment: 34
Effective length of query: 453
Effective length of database: 448
Effective search space:   202944
Effective search space used:   202944
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 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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