GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Aquimarina longa SW024

Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate WP_062057113.1 N456_RS11775 NADP-specific glutamate dehydrogenase

Query= curated2:B2RKJ1
         (445 letters)



>NCBI__GCF_001401755.1:WP_062057113.1
          Length = 447

 Score =  530 bits (1365), Expect = e-155
 Identities = 258/444 (58%), Positives = 332/444 (74%), Gaps = 2/444 (0%)

Query: 2   KTQEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRV 61
           K    M  + A++  E EFLQAV+EV  +V     ++  +    I+ R+VEP+R   FRV
Sbjct: 4   KIDAFMEEVRARNAHEPEFLQAVQEVAETVIPYIAKNEIYNGKNILLRMVEPERAIMFRV 63

Query: 62  PWVDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMG 121
           PWVDD+G++ VN GYR+Q N+AIGPYKGG+RFHPSVN+SILKFL FEQ+FKN+LTTLPMG
Sbjct: 64  PWVDDKGEIHVNRGYRIQMNSAIGPYKGGLRFHPSVNISILKFLAFEQVFKNSLTTLPMG 123

Query: 122 GGKGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKK 181
           GGKGG+DF PKGKS+ EIMRFC SFM+EL+R+IGPDTD+PAGDIGVGGRE+G++FGMY+K
Sbjct: 124 GGKGGSDFDPKGKSDDEIMRFCHSFMSELFRHIGPDTDVPAGDIGVGGREIGFLFGMYRK 183

Query: 182 LAREHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAW 241
           +  E TG LTGKG  +GGS +RPE+TG+G VYF +NM +  G  + GK + ISG GNVA 
Sbjct: 184 MRNEFTGVLTGKGLTWGGSLIRPEATGYGTVYFAKNMLETKGESFDGKIVTISGSGNVAQ 243

Query: 242 GVAQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQ 301
             A+KAT+LG K+VT+S   GY+YD DGI+  EK   +++L++     +S+Y  ++P+A+
Sbjct: 244 YAAEKATQLGGKIVTLSDSSGYIYDADGIDA-EKLAFVMELKNIKRGRISEYATKYPSAE 302

Query: 302 FFPGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANK 361
           F  GK PWE K D A+PCATQNE++ +DA TL  NG   ++E +NM  T EA   +   K
Sbjct: 303 FHQGKTPWEVKCDIALPCATQNELDGDDAATLIANGCVCISEGANMPSTPEAIAAFHKAK 362

Query: 362 MLFAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGN-Y 420
           + FAPGKA NAGGV+ SGLEMTQN++   WT EEVD  L QIM+DIH  C+ YG D + Y
Sbjct: 363 IFFAPGKASNAGGVATSGLEMTQNSLRYNWTREEVDDKLKQIMEDIHSACLEYGTDDDGY 422

Query: 421 IDYVKGANIAGFMKVAKAMVAQGV 444
           +DYVKGANIAGF+KVA AM+AQGV
Sbjct: 423 VDYVKGANIAGFVKVADAMLAQGV 446


Lambda     K      H
   0.319    0.137    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: 711
Number of extensions: 27
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: 445
Length of database: 447
Length adjustment: 32
Effective length of query: 413
Effective length of database: 415
Effective search space:   171395
Effective search space used:   171395
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 (21.7 bits)
S2: 51 (24.3 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