GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Shewanella loihica PV-4

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::C6KEM4
         (506 letters)



>FitnessBrowser__PV4:5211158
          Length = 506

 Score =  324 bits (831), Expect = 4e-93
 Identities = 190/497 (38%), Positives = 279/497 (56%), Gaps = 21/497 (4%)

Query: 13  FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72
           FIGG W  P  G      +P        +      D+E+A+ AA  A  +D    W +  
Sbjct: 22  FIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAA--KDA---WGKTS 76

Query: 73  GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEA-SGDMDDVAACFEYYADLAEALD 131
              R+N L  IA +++     LA+ ET ++GK + E  + D+      F Y+A    A +
Sbjct: 77  VTERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQE 136

Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191
           G      +    N  SY   EP+GVVG I PWN+PLLMA WK+APALAAG   +LKP+E 
Sbjct: 137 GSAADIDN----NTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 192

Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251
             VS L +  +  ++ LP GVLNI+ G G EAG  L+    + K+AFTGST+ G  I+  
Sbjct: 193 TPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKC 251

Query: 252 AAQMVKPVSLELGGKSPLIVFDDIGD-----IDKAVEWTMFGIFANAGQVCSATSRLLLH 306
           AA+ + P ++ELGGKSP I F D+ +     +DKAVE  +   F N G+VC+  SR+L+ 
Sbjct: 252 AAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLAFF-NQGEVCTCPSRVLIA 310

Query: 307 EKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGG 366
           E I  KF+D+++A AK IK  +PL+   ++G+  S+ Q++KI  ++   R+EGA +L GG
Sbjct: 311 ESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGG 370

Query: 367 GRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423
              Q       GF++EPTI+      M+++QEE+FGPVI V  F+ ++EA+ +ANDT YG
Sbjct: 371 TSCQLSGDQSSGFYIEPTILKG-HNKMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYG 429

Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYL 483
           L   V + D  R +R+ + + +G +WINC       A +GG K+SG GRE  +  L +Y 
Sbjct: 430 LGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQ 489

Query: 484 TVKQVTKYCSDEPWGWY 500
             K +       P G++
Sbjct: 490 NTKNLLVSYDVNPLGFF 506


Lambda     K      H
   0.318    0.136    0.418 

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: 653
Number of extensions: 32
Number of successful extensions: 6
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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