GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Marinobacter adhaerens HP15

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate GFF1133 HP15_1111 betaine aldehyde dehydrogenase

Query= SwissProt::Q9H2A2
         (487 letters)



>lcl|FitnessBrowser__Marino:GFF1133 HP15_1111 betaine aldehyde
           dehydrogenase
          Length = 493

 Score =  417 bits (1071), Expect = e-121
 Identities = 213/491 (43%), Positives = 318/491 (64%), Gaps = 9/491 (1%)

Query: 3   GTNALLMLENFIDGKFLP-CSSYI-DSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPS 60
           G  A+  +++ I+G+++  CSS + D+ +P+ G++  +V  +G++E++AAVKAAR A   
Sbjct: 4   GKAAMKEIKHHINGQYVSSCSSRLFDNVNPANGKIISKVHEAGREEVDAAVKAARAALRG 63

Query: 61  -WSSRSPQERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFAS 119
            W   +  ER+ +L++VAD +    +EF + E  D GK  ++A  +DIPR   NF+ FA 
Sbjct: 64  PWGKMTLDERTSILHKVADGINARFDEFLEGECLDTGKPKSMASHIDIPRGAANFKVFAD 123

Query: 120 SSLHHTSECTQM---DHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVI 176
              +  +E  +M   D  G ++Y VR P GV G+ISPWNLPL L+TWK+ PA+A GNTV+
Sbjct: 124 MIKNVPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVV 183

Query: 177 AKPSELTSVTAWMLCKLLDKAGVPPGVVNIVFGTG-PRVGEALVSHPEVPLISFTGSQPT 235
            KPSE T  T  +L +++ +AGVP GV N+V G G    G  L  HP+V  I+FTG   T
Sbjct: 184 VKPSEETPTTTTLLGEVMKEAGVPDGVFNVVHGFGGDSAGAFLTEHPQVDGITFTGEIGT 243

Query: 236 AERITQLSAPHCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFV 295
            E I + +A   + +SLELGGKN  ++F D ++D+ I  T+RS+FAN G++CL T R++V
Sbjct: 244 GEVIMKAAAKGIRDISLELGGKNAGVVFADCDIDKAIEGTMRSAFANCGQVCLGTERVYV 303

Query: 296 QKSIYSEFLKRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCG 355
           ++SI+ EF+ R  EA    K+G P D    +G L+S  H EKV SY ++A+ +GA +  G
Sbjct: 304 ERSIFDEFVGRLKEAAEGMKIGPPDDAEADMGPLVSLNHREKVLSYYQKAVDDGATVVTG 363

Query: 356 EGVDKLSLPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNV 415
            GV ++  P     G ++ PT+ T + ++S  +T+EIFGP   + PFD+EEE IE AN++
Sbjct: 364 GGVPEM--PEALAGGAWVQPTIWTGLPEDSAVITDEIFGPCCHIRPFDTEEEAIELANSL 421

Query: 416 KYGLAATVWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYD 475
            YGLA+ +WS N+ R HRVA ++++G++W N W +R+L  PFGG K SGIGREG   S +
Sbjct: 422 PYGLASAIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGIGREGGVHSLE 481

Query: 476 FFTEIKTITVK 486
           F+TE+K I VK
Sbjct: 482 FYTEMKNICVK 492


Lambda     K      H
   0.319    0.133    0.404 

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: 625
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: 487
Length of database: 493
Length adjustment: 34
Effective length of query: 453
Effective length of database: 459
Effective search space:   207927
Effective search space used:   207927
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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