Aligments for a candidate for patD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for patD in Pseudomonas stutzeri RCH2

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase

Query= BRENDA::P49189
         (494 letters)



>lcl|FitnessBrowser__psRCH2:GFF2584 Psest_2634 glycine betaine
           aldehyde dehydrogenase
          Length = 490

 Score =  467 bits (1202), Expect = e-136
 Identities = 240/476 (50%), Positives = 327/476 (68%), Gaps = 7/476 (1%)

Query: 24  DASGTE--KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAA 81
           DAS  E  ++  PA G V+A    +G  ++  AV++A+   +IW+  +G+ER RI+  A 
Sbjct: 17  DASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTGIERARIMRRAV 76

Query: 82  RIIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLPGGSFG 140
            ++RER DE+A +E ++ GK + E R +DI      LEYYAGLA ++ GE I L   SF 
Sbjct: 77  DLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEGEQIPLRDSSFV 136

Query: 141 YTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAG 200
           YTRREPLGV  GIGAWNYP QIA WK+APALA GNAM+FKPS  T +SAL LAEI+SEAG
Sbjct: 137 YTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSALKLAEIFSEAG 196

Query: 201 VPPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKG-IKPVTLELGGK 258
           +P G+FNV+ G GA  G  + +HP +AKVSFTG V TG K+M  +A   +K VT+ELGGK
Sbjct: 197 LPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSSLKDVTMELGGK 256

Query: 259 SPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIG 318
           SPLII  D D++ A   A+MANF + GQVC NGTRVFV   +   F  +++++ QRI++G
Sbjct: 257 SPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEAKLLERVQRIRLG 316

Query: 319 DPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVL 378
           DP  E+T  GPL++  H+  VL ++   K  GA++LCGG+  V E    K G ++ P + 
Sbjct: 317 DPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGE-RVTEGEYAK-GAFVAPTIF 374

Query: 379 TNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAEL 438
           ++C DDM  V EEIFGPV+S+L +  E EV+ RANDT +GLAAGV T D+ RAHR++  L
Sbjct: 375 SDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADLARAHRIIHRL 434

Query: 439 QAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494
           +AG C+IN +  SP ++P GGYK+SG GRENG  ++ +Y+++K+V VE+G+  S F
Sbjct: 435 EAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQVELGEFASVF 490


Lambda     K      H
   0.320    0.137    0.411 

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: 676
Number of extensions: 27
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 494
Length of database: 490
Length adjustment: 34
Effective length of query: 460
Effective length of database: 456
Effective search space:   209760
Effective search space used:   209760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Protein sequences (fasta format)
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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 preprint 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