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 GFF1133 HP15_1111 betaine aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Marino:GFF1133
          Length = 493

 Score =  332 bits (852), Expect = 1e-95
 Identities = 187/482 (38%), Positives = 284/482 (58%), Gaps = 15/482 (3%)

Query: 24  INGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKR 83
           ING+Y ++  +  F+ V+P     ++K+      ++D A+ AAR    RG W   +  +R
Sbjct: 15  INGQYVSSCSSRLFDNVNPANGKIISKVHEAGREEVDAAVKAARAAL-RGPWGKMTLDER 73

Query: 84  KAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVA 143
            ++L+K+AD + A  +E    E LDTGKP   +   DIP  A   + +A+ I  V  E  
Sbjct: 74  TSILHKVADGINARFDEFLEGECLDTGKPKSMASHIDIPRGAANFKVFADMIKNVPTESF 133

Query: 144 TTSSHE----LAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLS 199
              + +    L   VR P GVI  I PWN PLLL  WK+GPALA GN+V++KPSE++P +
Sbjct: 134 EMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPTT 193

Query: 200 AIRLAGLAKEAGLPDGVLNVVTGFGHE-AGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258
              L  + KEAG+PDGV NVV GFG + AG  L+ H  +D I FTG   TG+ ++K A  
Sbjct: 194 TTLLGEVMKEAGVPDGVFNVVHGFGGDSAGAFLTEHPQVDGITFTGEIGTGEVIMKAAA- 252

Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318
             ++ + LE GGK+A +VFADC D+ +A   T    F N GQVC+   R+ +E SI DEF
Sbjct: 253 KGIRDISLELGGKNAGVVFADC-DIDKAIEGTMRSAFANCGQVCLGTERVYVERSIFDEF 311

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA----- 373
           +  LK+ A+  + G P D    MG L+   H + V S+ ++    G  ++ G        
Sbjct: 312 VGRLKEAAEGMKIGPPDDAEADMGPLVSLNHREKVLSYYQKAVDDGATVVTGGGVPEMPE 371

Query: 374 GLA--AAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
            LA  A + PTI+  +  ++++  +EIFGP   +  F +EE+A++LAN   YGL +A+W+
Sbjct: 372 ALAGGAWVQPTIWTGLPEDSAVITDEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWS 431

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
            +++RAHR++ +++AG ++VN++   D+  PFGG KQSG GR+  +H+LE +TE+K I +
Sbjct: 432 ENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGIGREGGVHSLEFYTEMKNICV 491

Query: 492 SL 493
            L
Sbjct: 492 KL 493


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: 594
Number of extensions: 28
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: 493
Length adjustment: 34
Effective length of query: 461
Effective length of database: 459
Effective search space:   211599
Effective search space used:   211599
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