GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Aquimarina longa SW024

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_062053068.1 N456_RS01240 aldehyde dehydrogenase

Query= BRENDA::Q9RW56
         (523 letters)



>NCBI__GCF_001401755.1:WP_062053068.1
          Length = 480

 Score =  233 bits (593), Expect = 2e-65
 Identities = 147/468 (31%), Positives = 237/468 (50%), Gaps = 15/468 (3%)

Query: 55  IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARARILLKAAAILKRR 114
           I + NP  T E+      +++ D + A + A  AF SW    +  R+ IL K A+++   
Sbjct: 21  IDNYNP-STGEIYSLLPNSSVTDVQMAYEAAKTAFPSWSTTSLQHRSDILAKIASLIIEN 79

Query: 115 RLEACALMSIEVGKNYAEA-DVEVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGLM 173
                   +I+ GK  + A  V++  A    +++A +  ++A    +  +  +   N  +
Sbjct: 80  LELLANAEAIDNGKPLSLATSVDIPRASSNFDFFAHAITQFAS--EAHESMGQNAINFTL 137

Query: 174 SIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPA 233
             P+GV   ISPWN P  +F    A  + AGN VV KP+E   + A  + DI  +AGLP 
Sbjct: 138 RNPIGVVGCISPWNLPLYLFTWKIAPALAAGNTVVAKPSEITPMTAYLLGDICTKAGLPK 197

Query: 234 GVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELG 293
           GVL  + G+G   G+ +  H   + I+FTG  A G HI + AA +       K++ +ELG
Sbjct: 198 GVLNIVHGLGNTTGQAIIEHPDIKAISFTGGTATGAHIAKTAAPM------FKKLSLELG 251

Query: 294 GKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALK 353
           GK+  ++    D E  +T   + +F   GQ C   SR+ +  ++YD+    F+++ KALK
Sbjct: 252 GKNPNLIFADCDYEKMLTTTLRSSFANQGQICLCGSRIFIERTIYDQFKKDFIKKTKALK 311

Query: 354 MGTG-EENANVTAVVNQMSFNKIKGYLELAPSE-GKVLLGGEATGEANGKQGYYIQPTIV 411
           +G    +  N+ A+V++    K+K Y+++A  E G +L GG+       + GYY+QPTI+
Sbjct: 312 IGEPLNKETNIGALVSKSHLEKVKSYIDIAEQEGGTILYGGDYITVKGYENGYYLQPTII 371

Query: 412 GDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEF 471
              D N RL QEEIFGPVV ++       AL +AN+  YGL+  + +N+  R        
Sbjct: 372 EVTDSNCRLTQEEIFGPVVTIMPFDTDDQALSLANNVRYGLSATIWTNNLNRSMYLAKHI 431

Query: 472 EVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519
           + G ++ N  +   +    PFGG   SG   + GG + L  F + K V
Sbjct: 432 QAGIIWINTWMMRDL--RTPFGGVKDSGI-GREGGFEALRFFTEPKNV 476


Lambda     K      H
   0.317    0.134    0.391 

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: 542
Number of extensions: 25
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: 523
Length of database: 480
Length adjustment: 34
Effective length of query: 489
Effective length of database: 446
Effective search space:   218094
Effective search space used:   218094
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 (21.6 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