GapMind for catabolism of small carbon sources

 

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

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__ANA3:7025944
          Length = 482

 Score =  212 bits (540), Expect = 2e-59
 Identities = 141/465 (30%), Positives = 220/465 (47%), Gaps = 10/465 (2%)

Query: 56  NGSW--GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEI 113
           NG W      E +    PA    IA V     A+ +  +  A  A   W  + A +RG  
Sbjct: 16  NGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALPAWRALTAKERGVK 75

Query: 114 VRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSER 173
           +R+  + L E    L  +++ E GK L E  GEV       ++    ++ + G  +P  +
Sbjct: 76  LRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAEEAKRVYGDTIPGHQ 135

Query: 174 SGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKI 233
               ++    PVG+   IT +NFP A+     A A+  G   + K AP T   ++A    
Sbjct: 136 GDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALA---- 191

Query: 234 IAKVLEDNKLPGAICSLTCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGR 292
           +A + E   +P  + S+  G A  IG  M  +  V  LSFTGSTQVG ++         +
Sbjct: 192 LAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIKLMEQCAPTLKK 251

Query: 293 SLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKK 352
             LELGGN   I F+DA++   V  A+ A    AGQ C  A R+++   ++DE   +L  
Sbjct: 252 LSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFARKLSI 311

Query: 353 AYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPT 412
           A  +++VG      V  GPL    AV      +E+A  +G TVV GGK     GN+ EPT
Sbjct: 312 AVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGKPHSLGGNFFEPT 371

Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472
           ++T +     +A  ETF P+  +FKF + ++V    N+ + GL++  + +D+  +  W  
Sbjct: 372 VLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYGRDISLV--WKV 429

Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517
            +  + G+V VN      E+   FGG K +G GRE      ++Y+
Sbjct: 430 TEALEYGMVGVNTGLISTEV-APFGGMKSSGLGREGSKFGIEEYL 473


Lambda     K      H
   0.318    0.136    0.417 

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: 654
Number of extensions: 28
Number of successful extensions: 3
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: 539
Length of database: 482
Length adjustment: 34
Effective length of query: 505
Effective length of database: 448
Effective search space:   226240
Effective search space used:   226240
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 (21.7 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