GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pontimonas salivibrio CL-TW6

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_104912863.1 C3B54_RS01080 aldehyde dehydrogenase family protein

Query= BRENDA::Q65NN2
         (516 letters)



>NCBI__GCF_002950575.1:WP_104912863.1
          Length = 1180

 Score =  227 bits (579), Expect = 2e-63
 Identities = 141/432 (32%), Positives = 222/432 (51%), Gaps = 24/432 (5%)

Query: 77  EKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHEFSALLVKEAGKPWNEADADTA 136
           +  ++   +  + W     E R  +L +A A++  ++ E  +++++EAGK   E+D + +
Sbjct: 546 DSIVEKMRRGGKKWAARGAEGRGKILLKAAAELGVRRGEIMSVMMQEAGKTLAESDPEIS 605

Query: 137 EAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP 196
           EAIDF  YYA Q +E+           + N   +TP G+T+V PPWNF  AI  G+  + 
Sbjct: 606 EAIDFARYYASQAVEME----------QLNGAKFTPVGLTMVAPPWNFPVAIPTGSVTSA 655

Query: 197 IVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSIIT 256
           +  G+ V++KPA      AA  VE L  +G+PK V++    S  E+G  L+ H     + 
Sbjct: 656 LAAGSAVIIKPAPQVRRCAAVMVEALWAAGVPKDVLHLADVSEGELGRALISHQGVDRVI 715

Query: 257 FTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGF 316
            TG+       FE AA  +  +  L  V+AE  GK+ +V+    DI+LA   +  SAFG 
Sbjct: 716 LTGA-------FETAALFRSWRADL-PVLAETSGKNALVITPSADIDLAVADLVKSAFGH 767

Query: 317 AGQKCSAGSRAVVHEKV--YDEVLKRVIEITESKKVGEPDS-ADVYMGPVIDQASFNKIM 373
           AGQKCSA S  ++   V   +   +++ +   +  VG PD+  +  M P+I+        
Sbjct: 768 AGQKCSAASLVILVGSVAKSERFWRQLEDAVNTLDVGWPDARPETTMNPIIEPPGAKLRQ 827

Query: 374 DYIEIGKEEGRLVSGGKGDDSKGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDE 433
              E+G  E  L    + DD++  +  P +   + P +   Q E FGP++      +  +
Sbjct: 828 GLTELGAGEEWLAEPRQLDDTERLW-SPGVRLGVRPGSTFHQTEYFGPLLGVMTARTLQD 886

Query: 434 ALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMS-- 491
           A+E  N+ EYGLT  + + + D ++      H GNLY NR  TGAIV   PFGG+K S  
Sbjct: 887 AVEYQNSVEYGLTAGIHSLDPDEVSYWLDHVHAGNLYVNRGITGAIVRRQPFGGWKKSSV 946

Query: 492 GTDSKAGGPDYL 503
           G  +KAGGP+YL
Sbjct: 947 GPTAKAGGPNYL 958


Lambda     K      H
   0.315    0.133    0.382 

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: 1204
Number of extensions: 56
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: 516
Length of database: 1180
Length adjustment: 41
Effective length of query: 475
Effective length of database: 1139
Effective search space:   541025
Effective search space used:   541025
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: 55 (25.8 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