GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Marinobacter adhaerens HP15

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Marino:GFF4092
          Length = 486

 Score =  337 bits (865), Expect = 4e-97
 Identities = 189/483 (39%), Positives = 286/483 (59%), Gaps = 15/483 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           +ING+Y  +A    F+ V+P     ++K+      ++D A+ AAR    RG W   +  +
Sbjct: 7   YINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAAL-RGPWGKMTLEQ 65

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R A+L+K+AD + A  +E    E LDTGKP   +   DIP  A   + +A+ I  V  E 
Sbjct: 66  RTAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADMIKNVPTES 125

Query: 143 ATTSSHE----LAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198
               + +    L   VR P GVI  I PWN PLLL  WK+GPALA GN+V++KPSE++P 
Sbjct: 126 FEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPT 185

Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHE-AGQALSRHNDIDAIAFTGSTRTGKQLLKDAG 257
           +   L  + KEAG+PDGV NVV GFG + AG  L+ H  +D   FTG T TG+ ++K A 
Sbjct: 186 TTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEVIMKAAA 245

Query: 258 DSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317
              ++ + LE GGK+A +VFADC D+++A   T    F N GQVC+   R+ +E SI DE
Sbjct: 246 -KGIRDISLELGGKNAGLVFADC-DMEKAIEGTMRSAFANCGQVCLGTERVYVERSIFDE 303

Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN----- 372
           F+  LK+ A+  + G P D    +G L+   H + V S+ ++    G  ++ G       
Sbjct: 304 FVGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGGVPDMP 363

Query: 373 AGLA--AAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVW 430
           A LA  A + PTI+  +  ++++  +EIFGP   +  F +EE+A++LAN   YGL +A+W
Sbjct: 364 AELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIW 423

Query: 431 TRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490
           + +++RAHR++ +++AG ++VN++   D+  PFGG KQSG GR+  +H+LE +TE+K I 
Sbjct: 424 SENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGVGREGGVHSLEFYTEMKNIC 483

Query: 491 ISL 493
           + L
Sbjct: 484 VKL 486


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: 612
Number of extensions: 32
Number of successful extensions: 7
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: 486
Length adjustment: 34
Effective length of query: 461
Effective length of database: 452
Effective search space:   208372
Effective search space used:   208372
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