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-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF4232 Psest_4305 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__psRCH2:GFF4232 Psest_4305 NAD-dependent
           aldehyde dehydrogenases
          Length = 497

 Score =  582 bits (1500), Expect = e-170
 Identities = 292/492 (59%), Positives = 361/492 (73%), Gaps = 4/492 (0%)

Query: 6   LAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSA 65
           LA WQ +A  L IE R FI GEY AAA+   F+ + PV    LA++A  +  D +RA+++
Sbjct: 6   LADWQQRARDLHIEGRAFIQGEYCAAADGGQFDCISPVDGRVLAQVASCEQADAERAVAS 65

Query: 66  ARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAA 125
           AR  F+ G WS  +PAKRKAVL + ADL+EA+ EELALLETLD GKPI  SL  DIPGAA
Sbjct: 66  ARAAFDAGSWSRLAPAKRKAVLIRFADLLEANREELALLETLDMGKPIGDSLAVDIPGAA 125

Query: 126 RAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAG 185
           RA+RW  EAIDK+Y EVA T   +L ++ REPVGV+AAIVPWNFPL++ CWKLGPALA G
Sbjct: 126 RALRWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVAAIVPWNFPLMMACWKLGPALATG 185

Query: 186 NSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGS 245
           NSV+LKPSEKSPL+AIR+A LA +AG+P GVLNV+ G+GH  G+AL+ H D+D + FTGS
Sbjct: 186 NSVVLKPSEKSPLTAIRIAQLAIDAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGS 245

Query: 246 TRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAG 305
           TR  KQL+  AG+SNMKRVWLEAGGKS NIVFAD PDLQ AA A A  I +NQG+VC AG
Sbjct: 246 TRVAKQLMIYAGESNMKRVWLEAGGKSPNIVFADAPDLQAAAQAAAGAIAFNQGEVCTAG 305

Query: 306 TRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQ 365
           +RLL+E SI + FL ++ +  + W+PG+PLDPAT +G L+D    ++V  +I  G   G 
Sbjct: 306 SRLLVERSIRERFLPMVVEALKGWKPGNPLDPATNVGALVDTQQLNTVLGYIDAGRQAGA 365

Query: 366 LLLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421
            +L G    L    G    PTIF  VD    +++EEIFGPVL V  F S E+A+ +AND+
Sbjct: 366 QVLIGGQRTLEETGGLYVEPTIFDGVDNAMRIAQEEIFGPVLSVITFDSAEEAVAIANDT 425

Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481
            YGL AAVWT DLS+AHR +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA +
Sbjct: 426 PYGLAAAVWTADLSKAHRTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFD 485

Query: 482 KFTELKTIWISL 493
           K+TELK  WI L
Sbjct: 486 KYTELKATWIQL 497


Lambda     K      H
   0.317    0.133    0.389 

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: 649
Number of extensions: 19
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: 495
Length of database: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
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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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 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