GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS05620
          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 (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