GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Erythrobacter marinus HWDM-33

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_047092853.1 AAV99_RS05730 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_001013305.1:WP_047092853.1
          Length = 498

 Score =  208 bits (530), Expect = 3e-58
 Identities = 151/463 (32%), Positives = 237/463 (51%), Gaps = 24/463 (5%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI G  + +    T +  +P T    A++A G +  +DRAM  A+ V  + +W+ ++P K
Sbjct: 7   FIQGG-SGSGSGRTHKIWNPSTGEVQAEVALGDAALLDRAMENAKKV--QPEWAATNPQK 63

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  V+ K  +L+EA+ ++LA L + + GK +  + + D+      I +       + GE 
Sbjct: 64  RARVMFKFKELIEANMQDLAELLSSEHGKVVDDA-KGDVQRGLEVIEYACGIPQVLKGEY 122

Query: 143 ATTSSHELAMI-VREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201
              +   + +   R+P+G+ A I P+NFP ++  W  G A+AAGN+ ILKPSE+ P   +
Sbjct: 123 TQGAGPGIDVYSTRQPLGIGAGITPFNFPAMIPMWMFGMAIAAGNAFILKPSERDPSVPV 182

Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261
           RLA L  EAG P+G+L VV G   E   A+  H DI A++F GS+    Q +   G +N 
Sbjct: 183 RLAELFLEAGAPEGLLQVVHG-DKEMVDAILDHPDIAAVSFVGSSDIA-QYIYSRGTANA 240

Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLL-LEESIADEFLA 320
           KRV    G K+  +V  D  DL Q  +  A   F + G+ C+A   ++ + E  A+    
Sbjct: 241 KRVQAFGGAKNHGVVMPDA-DLDQVVNDLAGAAFGSAGERCMALPVVVPVGEDTANRLRE 299

Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESK-GQLLLDGRNAGLAA-- 377
            L       + G   DP    G ++   H   +  +I   E++ G++++DGR   L    
Sbjct: 300 KLIPAINALRIGVSNDPDAHYGPVVTPEHKARIEEWITTAENEGGEIVVDGRGYSLQGHE 359

Query: 378 ---AIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDL 434
               +GPT+   V P     +EEIFGPVL + R T  E AL+L ++ QYG G A++TR+ 
Sbjct: 360 KGFFVGPTLIDHVTPEMESYKEEIFGPVLQIVRATDFEHALRLPSEHQYGNGVAIFTRNG 419

Query: 435 SRAHRMSRRLKAGSVFVNNYNDGDMTVP-----FGGYKQSGNG 472
             A   + R+  G V +N      + VP     FGG+K+SG G
Sbjct: 420 HAAREFASRVNVGMVGIN----VPIPVPVAYHSFGGWKRSGFG 458


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: 547
Number of extensions: 35
Number of successful extensions: 6
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: 498
Length adjustment: 34
Effective length of query: 461
Effective length of database: 464
Effective search space:   213904
Effective search space used:   213904
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