Aligments for a candidate for adh in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized)
to candidate Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1

Query= SwissProt::P40047
         (520 letters)



>lcl|FitnessBrowser__Cola:Echvi_1300 Echvi_1300
           delta-1-pyrroline-5-carboxylate dehydrogenase, group 1
          Length = 543

 Score =  176 bits (446), Expect = 2e-48
 Identities = 137/433 (31%), Positives = 210/433 (48%), Gaps = 19/433 (4%)

Query: 83  VDEAVAAAKKAFETKWSIVEPEVRAKALFNLADLVE-KHQETLAAIESMDNGKSLFCARG 141
           V++A+ AA  A E  W  +E E RA      ADL+   ++  + A   +   K+ F A  
Sbjct: 81  VEQAINAALGAKEA-WETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSKNAFQAEI 139

Query: 142 DVAL-VSKYLRSCGGWADKIYGNVID-TGKNHFTYSIKEPL-GVCGQIIPWNFPLLMWSW 198
           D A  +  +LR    +  +IY      +G   +    + PL G    + P+NF  +  + 
Sbjct: 140 DSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNFTAIAGNL 199

Query: 199 KIGPALATGNTVVLKPAETTPLSALFASQLCQEAGIPAGVVNILPGSGRVVGERLSAHPD 258
              PA+  GNTVV KPA T   +A    Q+ +EAG+P GV+N++   G   GE +  HP+
Sbjct: 200 PTAPAMM-GNTVVWKPAYTQIYTANLLMQVFREAGVPDGVINLVYVDGPAAGEVIFEHPE 258

Query: 259 VKKIAFTGSTATGRHIMKVAADTVKK------VTLELGGKSPNIVFADADLDKAVKNIAF 312
              I FTGSTA  + I K   + ++K      +  E GGK   I    AD  +    +  
Sbjct: 259 FAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKSADAKQLATGLVR 318

Query: 313 GIFYNSGEVCCAGSRIYIQDTVYEEVLQKLKDYTESLKVGDPFDEEVFQGAQTSDKQLHK 372
           G F   G+ C A SR YI   ++E+V + +++   S+K+G P D   F  A   +K   K
Sbjct: 319 GAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGPEDFSNFINAVIDEKSFDK 378

Query: 373 ILDYVDVAKSEGARLVTGGARHGSKGYFVKPTVFADVKEDMRIVKEEVFGPIVTVSKFST 432
           I  Y+D AKS+G  +V GG    SKGYFV+PTV          + EE+FGP++T+  +  
Sbjct: 379 IAKYIDTAKSDGLEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPVLTIYVYQE 438

Query: 433 --VDEVIAMAND-SQYGLAAGIHTNDINKAVDVSKRVK--AGTVWIN--TYNNFHQNVPF 485
              +E + + +  S YGL   I ++D   A   +++++  AG  +IN           PF
Sbjct: 439 DHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTGAVVGQQPF 498

Query: 486 GGFGQSGIGREMG 498
           GG  +SG   + G
Sbjct: 499 GGARKSGTNDKAG 511


Lambda     K      H
   0.317    0.134    0.390 

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: 667
Number of extensions: 35
Number of successful extensions: 2
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: 520
Length of database: 543
Length adjustment: 35
Effective length of query: 485
Effective length of database: 508
Effective search space:   246380
Effective search space used:   246380
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 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources