GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF1133
          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 (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