GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sphingomonas indica Dd16

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_157123692.1 B9N75_RS04360 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_900177405.1:WP_157123692.1
          Length = 502

 Score =  385 bits (988), Expect = e-111
 Identities = 210/481 (43%), Positives = 296/481 (61%), Gaps = 12/481 (2%)

Query: 21  RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80
           +LFI+GE+  ++  +     DP T   +  I      D+DRA++AAR  F+ G WS   P
Sbjct: 26  KLFIDGEWVESSHGKRIPVFDPSTGKEIVAIVDASDADVDRAVAAARRAFDDGRWSGLPP 85

Query: 81  AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140
            +R+ ++ KLADL+EA+  E+A +E++D GKP   S   D+P    A+R+ A    K+ G
Sbjct: 86  YQRQRLVEKLADLLEANIPEIAEIESIDNGKPRSASQGYDLPKCVAALRYMAGWATKLTG 145

Query: 141 E------VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSE 194
           E      + T S H  A + REP+GV A IVPWNFPL++   K+ PAL+AG +V+LKP+E
Sbjct: 146 EHIEPSGMPTGSIH--AYVRREPIGVAAQIVPWNFPLMMAVQKIAPALSAGCTVVLKPAE 203

Query: 195 KSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLK 254
           ++ LSA+R A L  EAG+P GVLN+VTG G  AG  L RH D+D +AFTGST  GK ++ 
Sbjct: 204 QTSLSALRFADLVAEAGIPAGVLNIVTGDGETAGDRLVRHPDVDKVAFTGSTEVGK-IIN 262

Query: 255 DAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESI 314
            A    +KRV LE GGKS  IV  D  D+++ A+  A  IF N GQVCIAG+RL     +
Sbjct: 263 RAATDTLKRVTLELGGKSPVIVLPDV-DIEKTAAGAARSIFANAGQVCIAGSRLFAHRDV 321

Query: 315 ADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN-- 372
            D+ L ++   A  W+ G  L P T MG L+     + V  +I +G   G  +L G +  
Sbjct: 322 FDKLLEVVADNAGKWKVGPSLAPDTMMGPLVSTEQHERVLGYIDQGRKAGATVLAGGDTP 381

Query: 373 AGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTR 432
            G    + PTI VDV+P+ S+ REEIFGPVL   RF   +   + AND+ YGL A+VWTR
Sbjct: 382 GGDGWFVNPTILVDVNPDMSVVREEIFGPVLTAQRFDDLDAVAKAANDTNYGLAASVWTR 441

Query: 433 DLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492
           D+S  H+++ ++KAG V+ N  +  D ++PFGG+KQSG GR+   + +E +TELKT+ I+
Sbjct: 442 DVSAMHKLAAKVKAGMVWGNCPSAADTSLPFGGFKQSGFGRESGRYGIEAYTELKTVAIA 501

Query: 493 L 493
           L
Sbjct: 502 L 502


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: 628
Number of extensions: 26
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: 502
Length adjustment: 34
Effective length of query: 461
Effective length of database: 468
Effective search space:   215748
Effective search space used:   215748
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 24 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