GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Cupriavidus basilensis 4G11

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate RR42_RS27780 RR42_RS27780 betaine-aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Cup4G11:RR42_RS27780
          Length = 483

 Score =  386 bits (991), Expect = e-111
 Identities = 203/474 (42%), Positives = 295/474 (62%), Gaps = 6/474 (1%)

Query: 22  LFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81
           L I+G+       E    ++P T+ P+A +A+G + D+D A+SAAR   +   W     A
Sbjct: 12  LLIDGKRLPPGTGEYSTDINPATELPIALVAQGSAADVDLAVSAARAALKV--WCGLRAA 69

Query: 82  KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141
           +R  +L + ADL+EA+ EEL  LE+LD GKP+    R D+P     +R+YA   DK+ G+
Sbjct: 70  ERGRILYRFADLLEANQEELTALESLDAGKPLAAVRRQDMPAVIDTVRYYAGWADKINGQ 129

Query: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201
           V  T    L   VREPVGV+AAIVPWNFPL++  WK+ PALA G ++I+KP+E +PL+A+
Sbjct: 130 VVPTRPGALTYTVREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTAL 189

Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261
           R+  LA +AGLP GVLN+VTG G   G AL  H  ID + FTGS   G+ +++ A  +N 
Sbjct: 190 RVGELALQAGLPPGVLNIVTGKGSVVGNALVAHPGIDKVTFTGSPGVGRGIMQGAA-ANF 248

Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321
           KR+ LE GGKSAN++FAD  ++  A  A A+GIF+N GQVC AG+R+L +  + DE +  
Sbjct: 249 KRITLELGGKSANLIFADA-NVDAAVRAAASGIFFNAGQVCSAGSRILAQREVYDEVVEK 307

Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG--RNAGLAAAI 379
           L  +A + + G P  P TTMG L+      +V  ++  G+ +G + + G  R  G    +
Sbjct: 308 LAARAASIRVGDPAAPDTTMGPLVSSTQMKTVLDYVEIGKREGAIAVTGGERVGGKGYYV 367

Query: 380 GPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439
            PT+F +V     +S+EEIFGPV  V RF  E  A+++AN + + L A VW+ D+ R H+
Sbjct: 368 QPTVFANVGHEMRVSQEEIFGPVASVIRFEDEADAVRIANGTAFSLAAGVWSADIGRVHQ 427

Query: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493
           ++  LKAG+V++N Y   D+ +P+GG   SG GR+    A++ FTE K IW+SL
Sbjct: 428 VAAELKAGTVWINTYGHTDVRLPWGGAGDSGLGREHGDAAIDNFTEPKAIWLSL 481


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: 599
Number of extensions: 27
Number of successful extensions: 5
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: 483
Length adjustment: 34
Effective length of query: 461
Effective length of database: 449
Effective search space:   206989
Effective search space used:   206989
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