GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF4232
          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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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