GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pantoea rwandensis LMG 26275

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_084934223.1 HA51_RS09135 aldehyde dehydrogenase

Query= curated2:Q9K5Z5
         (515 letters)



>NCBI__GCF_002095475.1:WP_084934223.1
          Length = 478

 Score =  261 bits (668), Expect = 3e-74
 Identities = 166/474 (35%), Positives = 250/474 (52%), Gaps = 18/474 (3%)

Query: 41  INGERVTT--DDKIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERA 98
           ING  V    D  I  +NPA  E ++  + + ++     A  +AE A   W+ +   ER 
Sbjct: 9   INGAFVADQHDKWIEVINPAT-EALLSRIPEGTKHDAAQAIAAAEAAQPGWEALPAIERG 67

Query: 99  NILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKDGKPVN 158
           N L + AA IR  + E +A +V E GK    A  +     D+LEY A +     +G+ VN
Sbjct: 68  NWLRKIAAGIRHHESELTATIVAEGGKTQGLAQTEVLFTADYLEYMA-EWARRYEGEIVN 126

Query: 159 S-REGEHNRYFYTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKF 217
           S R  E+   F   IGV   I PWNF   ++A      +VTGNT+ +KP+  TP  AA F
Sbjct: 127 SDRPNENIFVFKKAIGVTTGILPWNFPFFLIARKAAPALVTGNTIAIKPSELTPNNAAIF 186

Query: 218 VEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQ 277
            +++ E GLPKGV+NFV G G ++G  L  +P   L++ TGS   G+   + AA      
Sbjct: 187 AQIIHEIGLPKGVINFVYGYGPEVGQELAANPAVGLVSLTGSVGAGIATMQAAA------ 240

Query: 278 QHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVL 337
           +++ +V +E+GGK   +V  DADLDLA ++IV+S    +GQ C+   R  + + +YD  +
Sbjct: 241 KNVTKVSLELGGKAPAIVMDDADLDLAVKAIVSSRVINTGQVCNCAERVYVQEGIYDRFI 300

Query: 338 EKAVALTKQLSVGEPT-APDVYMGPVVDQGAFSKIMSYI-EVGKEEGRLMVGGEGDDSKG 395
               A  KQ+  G P    D+ MGP++ + A  ++   +     E G +++GG+   ++G
Sbjct: 301 TALTAAMKQVKFGNPAEQTDIDMGPLITEAALGRVEKKVANAVAEGGTVVLGGKRVGNQG 360

Query: 396 FFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHH 455
           F+ +PTI   V     IMQEEIFGPV+     +  D A+E+AN+ EYGLT ++ T N + 
Sbjct: 361 FYFEPTIITGVRQEMEIMQEEIFGPVLPVMAFKTLDEAIELANDCEYGLTSSIYTQNLNT 420

Query: 456 IEKAKRDFHVGNLYFNRNCTGAIVGYHPFGGFKMS---GTDSKAGGPDYLALHM 506
              A R    G  Y NR    A+ G+H   G++ S   G D + G  +YL  H+
Sbjct: 421 AMIALRKLKFGETYVNRENFEAMQGFH--AGWRKSGVGGADGRHGLEEYLQTHV 472


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: 563
Number of extensions: 31
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: 478
Length adjustment: 34
Effective length of query: 481
Effective length of database: 444
Effective search space:   213564
Effective search space used:   213564
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