GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Moritella dasanensis ArB 0140

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_017221244.1 A923_RS0108515 betaine-aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000276805.1:WP_017221244.1
          Length = 487

 Score =  310 bits (795), Expect = 6e-89
 Identities = 176/479 (36%), Positives = 271/479 (56%), Gaps = 13/479 (2%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           +++G+  A    ETFE ++P T A    +    +     A+ +A+  F    WS  +P +
Sbjct: 9   YVHGQSIANETGETFEVINPATGAVSYLVEVADASVQQAAIDSAKAGFST--WSKMTPME 66

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L K   L+    +ELA +E  DTGKP + +   D+   A +I ++A     + G  
Sbjct: 67  RSRILLKAVALLRERNDELAAIEVQDTGKPWQEASVVDVVTGADSIEFFAGLAPSIEGNQ 126

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
                 +     REP+G+ A I  WN+PL + CWK  PALA GN +I KPSE++P  AI+
Sbjct: 127 QQVGD-DFYYTRREPLGICAGIGAWNYPLQIACWKAAPALACGNVMIFKPSEETPRGAIK 185

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           LA +  +AG+P GV NVV G G   G  L+ H +I  ++FTG   TGK+++  A  S +K
Sbjct: 186 LAEVFTDAGVPHGVFNVVQGDGR-VGAWLTTHEEIAKVSFTGEVGTGKKVMAAAAGS-LK 243

Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322
           +V +E GGKS  I+F D  D+  A SA     FY QG+VC  GTR+ ++++I   F+  L
Sbjct: 244 QVTMELGGKSPLIIFDDA-DVDNAVSAAMLANFYTQGEVCTNGTRVFVQDAIYPRFIEKL 302

Query: 323 KQQAQN-WQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGR------NAGL 375
           +Q+ +N    G P+DP T  G LI   H   V +FI  G+++G  LL G       NA  
Sbjct: 303 RQRTENNIICGDPMDPETNFGALISKDHQQKVLNFIEIGKAEGAELLTGGHALKPDNAPN 362

Query: 376 AAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435
              + PTIF       +LS+EEIFGPV+ V  F+ E++ ++ AND++ GL A V+T+D++
Sbjct: 363 GYFVAPTIFTQCTDEMTLSKEEIFGPVMSVLTFSDEDEVVRRANDTRLGLAAGVFTQDIT 422

Query: 436 RAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISLE 494
           RAHR+  +++AG  ++N Y      +P GGYK SG GR+     L+ +T++K +++ ++
Sbjct: 423 RAHRVIHQMEAGICWINAYGASPAEMPVGGYKMSGIGRENGSETLKAYTQIKAVYVGMQ 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: 571
Number of extensions: 30
Number of successful extensions: 8
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: 487
Length adjustment: 34
Effective length of query: 461
Effective length of database: 453
Effective search space:   208833
Effective search space used:   208833
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