GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pantoea rwandensis LMG 26275

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_084931611.1 HA51_RS01965 aldehyde dehydrogenase

Query= BRENDA::Q9RW56
         (523 letters)



>NCBI__GCF_002095475.1:WP_084931611.1
          Length = 498

 Score =  217 bits (553), Expect = 7e-61
 Identities = 153/474 (32%), Positives = 230/474 (48%), Gaps = 29/474 (6%)

Query: 55  IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFES--WKKWDMDARARILLKAAAILK 112
           +++ NP  T EV+   A     D   A+QGA  AFES  W +     R  +LLK A +L+
Sbjct: 38  LETTNPA-TGEVLAHIAACNGHDVNTAVQGARSAFESGSWSQLHPGERKAVLLKLADLLE 96

Query: 113 RRRLEACALMSIEVGKNYAEA-DVEVAEAIDFLEYYARSAMKY----AGFGSSETTWFEG 167
               +   + S++ GK  +E   V+V E I  + ++A +  K     A  GS        
Sbjct: 97  NEVTQLAVMESLDSGKPVSECLAVDVPETIHVIRWHAEAIDKLYDQTAPAGSGAMAMIVR 156

Query: 168 EENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILR 227
           E       P+GV   + PWNFP  +        + AG  V+VKPAE   L A  + ++  
Sbjct: 157 E-------PIGVVGCVLPWNFPLLMLAWKIGPALAAGCSVIVKPAEQTSLTALRVAELAH 209

Query: 228 EAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKR 287
           EAG+PAGVL  + G GK+VGE +  HA    ++FTGS A G      +A+       +K+
Sbjct: 210 EAGIPAGVLNIVTGTGKDVGEPIGLHADIDMVSFTGSTATGRRFLHYSAESN-----LKK 264

Query: 288 VIMELGGKDGLIV-DETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFV 346
           +++E GGK+  +V D+  D+ +       GAF   G+ CSA SRL+V ++V D+++    
Sbjct: 265 IVLECGGKNPAVVFDDADDLASVAANVLSGAFWNMGENCSATSRLLVHENVKDKLLALIA 324

Query: 347 ERAKALKMGTGEENAN-VTAVVNQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYY 405
           E+    +MG   +  N +  ++    F K+  YL+ A  EG  ++ G  T      +G Y
Sbjct: 325 EQIGDWRMGNPLDPENRLGTMITAEHFCKVSDYLKTARKEGLRIIQGGFT-----DRGIY 379

Query: 406 IQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLE 465
           +QPTIV  V   S L +EEIFGPV+ V   K   +A+ +AN T+YGL   V +    R  
Sbjct: 380 VQPTIVDGVTPKSALFREEIFGPVLCVTTFKTEAEAIALANDTDYGLAASVYTGKLSRAI 439

Query: 466 QARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519
           +       G +  N    G      PFGGY  SG   +      L  + +LKT+
Sbjct: 440 RVSRAIRAGTVTVN--CFGEGDATTPFGGYKQSGFGGRDKSVYALDQYTELKTI 491


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: 587
Number of extensions: 30
Number of successful extensions: 5
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: 498
Length adjustment: 34
Effective length of query: 489
Effective length of database: 464
Effective search space:   226896
Effective search space used:   226896
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.

Links

Downloads

Related tools

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