GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Shewanella sp. ANA-3

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= curated2:Q2SXN9
         (487 letters)



>FitnessBrowser__ANA3:7025944
          Length = 482

 Score =  189 bits (480), Expect = 2e-52
 Identities = 142/463 (30%), Positives = 219/463 (47%), Gaps = 8/463 (1%)

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

Query: 62  RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK- 120
           R   ++R+  LL E  + LA M+  E GKPL EA+ EV   A+ ++          G+  
Sbjct: 72  RGVKLRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAEEAKRVYGDTI 131

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

Query: 181 TVEIWRDAGLPAGVLNLVQGEK-DTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239
              +   AG+PAGV +++ G+    G  + ++  +  L FTGS+  G  L +Q     + 
Sbjct: 192 LAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIKLMEQCAPTLK- 250

Query: 240 VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARL 299
            L+LE+GGN P +V +  +IDAAV  A+ + + +AGQ C CA RI V  G + D F  +L
Sbjct: 251 KLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVY-DEFARKL 309

Query: 300 ADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALGFV 359
           +    K+       +     G +I+  A  ++ +     +  GA+ +   K       F 
Sbjct: 310 SIAVGKLKVGEGIGEGVT-TGPLINCAAVEKVQSHLEDALSKGATVVAGGKPHSLGGNFF 368

Query: 360 NAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHT 418
              +L +V +   +  EE FGPLA + ++TD+DD I +ANDT FGL+A     D      
Sbjct: 369 EPTVLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYGRDISLVWK 428

Query: 419 FRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461
              A+  G+V  N     ++  APFGG   SG  R  + +  +
Sbjct: 429 VTEALEYGMVGVNTGLI-STEVAPFGGMKSSGLGREGSKFGIE 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: 488
Number of extensions: 20
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.

Links

Downloads

Related tools

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