GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF2584
          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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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