GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Amycolatopsis halophila YIM 93223

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= curated2:Q9K5Z5
         (515 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  254 bits (649), Expect = 5e-72
 Identities = 160/490 (32%), Positives = 251/490 (51%), Gaps = 34/490 (6%)

Query: 39  LVINGERVTTDDKI---VSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHT--WKNVN 93
           L I+G  V T       V +NPA   + +  V +A  + VD A  +A  AF    W+   
Sbjct: 4   LFIDGRWVDTTGTAPARVVLNPANAAE-LATVCEADEKDVDAAVAAARRAFDDSPWRATT 62

Query: 94  PEERANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKD 153
             ER  +L   A +++R K   +     + GK   E   D  +      YYA  +   + 
Sbjct: 63  ARERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYAN-LADNEA 121

Query: 154 GKPVNSREGEH-NRYFYTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPV 212
           G+ V++ +    +R  + P+GVC  I+PWN+ L  M+      +  GNTV++KP+  TP+
Sbjct: 122 GRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPL 181

Query: 213 VAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAV 272
              + + ++EEAG+P GVVN V G G ++G  ++ HP   L++FTG  + G ++   AA 
Sbjct: 182 TTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAA- 240

Query: 273 VHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDV 332
                + +KRV +E+GGK+  VV  DAD D A    + +AF  SGQ CSAGSR ++  D+
Sbjct: 241 -----EGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDI 295

Query: 333 YDVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGG--- 388
           +D  + +       + +G+   P    GP+       K+  +IE  K EG RL+VGG   
Sbjct: 296 HDEFVAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRP 355

Query: 389 -EGDDSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGA 447
            E + + G+F++PT+FAD D   RI+Q+E+FGPVV   +    D A+ +AN+TEYGL GA
Sbjct: 356 TEPELADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGA 415

Query: 448 VITTNRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPF------GGFKMSGTDSKAGGPDY 501
           V T++    ++       G ++ N         +HP+      GGF  SG   +  GP  
Sbjct: 416 VWTSDASRAQRVAGALRHGTVWIN--------DFHPYLPQAEWGGFGKSGIGREL-GPSG 466

Query: 502 LALHMQAKTV 511
           L  + + K +
Sbjct: 467 LEEYRETKHI 476


Lambda     K      H
   0.318    0.135    0.394 

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: 629
Number of extensions: 29
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: 515
Length of database: 496
Length adjustment: 34
Effective length of query: 481
Effective length of database: 462
Effective search space:   222222
Effective search space used:   222222
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