GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Mariniradius saccharolyticus AK6

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_008626729.1 C943_RS08810 Glu/Leu/Phe/Val dehydrogenase

Query= BRENDA::P00366
         (558 letters)



>NCBI__GCF_000330725.2:WP_008626729.1
          Length = 472

 Score =  447 bits (1150), Expect = e-130
 Identities = 232/455 (50%), Positives = 304/455 (66%), Gaps = 14/455 (3%)

Query: 103 RSILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVK 162
           + +L  IK CN +    FPIR +DG++EV+ GYR QHS H+ P KGGIR+S+ V  +EVK
Sbjct: 28  QGLLDQIKACNSIYKFHFPIRHEDGTYEVLTGYRIQHSHHKLPVKGGIRFSSFVDEEEVK 87

Query: 163 ALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVP 222
            LA+LMTYKCA+V+VPFGGAK GV + PKNY +  LEKITRR+T EL KK FIGP +DVP
Sbjct: 88  GLAALMTYKCALVNVPFGGAKGGVSVEPKNYNERMLEKITRRYTSELIKKKFIGPAIDVP 147

Query: 223 APDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIEN 282
           APD  TG REM+WI DTY        INA  CVTGKP+SQ GI GR  ATG+GVF GI  
Sbjct: 148 APDYGTGAREMAWIVDTY-EAFNPEVINAKGCVTGKPLSQHGIEGRTEATGQGVFFGIRE 206

Query: 283 FINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCITVGESDGSIWNPDG 342
            +     M  LG+T G+  KT +VQG GNVG +S +Y+   GAK I V E +G IW+  G
Sbjct: 207 ALAVEEDMRELGLTTGYRGKTVIVQGLGNVGYYSAKYIAEAGAKVIGVAEWNGGIWDEKG 266

Query: 343 IDPKELEDFKLQHGTILGFPKAKIYEGSI--LEVDCDILIPAASEKQLTKSNAPRVKAKI 400
           ID + L++++L++    GFPK +  E SI  L   CDILIPAA E Q+TK NAP+++AKI
Sbjct: 267 IDIEALKEYQLKNKGFKGFPKGEFIENSIEMLTYPCDILIPAALENQITKDNAPKIQAKI 326

Query: 401 IAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYER 460
           I E ANGP T EA+KI LE+ IMVIPD+YLNAGGVTVSYFEWL NL+ VS+G+L  +Y++
Sbjct: 327 IGEAANGPVTKEAEKILLEKGIMVIPDMYLNAGGVTVSYFEWLKNLSRVSFGKLERRYDQ 386

Query: 461 DSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQ 520
           +    LL +++ +   +F +           E    I GASE+D+V SGL  TM  +   
Sbjct: 387 EKFRRLLGTIENATGEEFTED----------EKTQLIQGASERDLVLSGLEETMVTAYHA 436

Query: 521 IMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGV 555
           I R   + N+   LRTA ++ A++++ + Y + G+
Sbjct: 437 INRVRKEKNI-KSLRTAGFILALQRIAQSYTDLGI 470


Lambda     K      H
   0.318    0.136    0.404 

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: 707
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: 558
Length of database: 472
Length adjustment: 35
Effective length of query: 523
Effective length of database: 437
Effective search space:   228551
Effective search space used:   228551
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 24 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