Aligments for a candidate for gadh2 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh2 in Herbaspirillum seropedicae SmR1

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate HSERO_RS22810 HSERO_RS22810 alcohol dehydrogenase

Query= BRENDA::Q5FRK5
         (437 letters)



>FitnessBrowser__HerbieS:HSERO_RS22810
          Length = 423

 Score =  355 bits (911), Expect = e-102
 Identities = 182/403 (45%), Positives = 252/403 (62%), Gaps = 18/403 (4%)

Query: 20  TAQDSDKAIVEKGRYLAAASDCAACHSVHGKPEYSGGVSFSLPMGKIYSTNITPDPDHGI 79
           TAQ +D+ +V +G+YLA A DC ACHS  GKP YSGG++     G IYSTNITPD +HGI
Sbjct: 23  TAQAADQDLVARGQYLARAGDCMACHSAAGKPAYSGGLAIDSGHGIIYSTNITPDKEHGI 82

Query: 80  GRYTEAQFGQALRQGIRRDGSTLYPAMPFPSYARLTDSDIHALFVYFRDGVKAVPVSAPR 139
           G Y+EAQF  A+R G+R DG+ LYPAMP+PSYA+++D DIHAL+ YF  GV+ V  + P 
Sbjct: 83  GNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDEDIHALYTYFMQGVQPVASTPPA 142

Query: 140 NEIPWPLSIRWPLTFWRWAFA-PTPHKAITSTAGEFTDPLLARGAYLVEGPAHCGACHSP 198
           + + +P +IRW +  W   FA   P +     + E     + RGAYLVEG  HCG+CH+P
Sbjct: 143 SSMSFPFNIRWGMKLWNVFFANDKPFREQDGWSAE-----IKRGAYLVEGLGHCGSCHTP 197

Query: 199 RAITMQEKALIAHDGSLYLAGGAPVDGWTPPSLRQENRTGLGRWSEEDIVSFLRTGRSNP 258
           R + M EKA  +     +L+GG  ++GW  PSLR     G+  WS +DIV +L+TGR+  
Sbjct: 198 RGVAMNEKASDSSQAQ-FLSGG-DLNGWAVPSLR-----GMPHWSAQDIVDYLQTGRNKT 250

Query: 259 GSVFGSMTSAVLHGTQKLTDNDLHAIAHYLKSLPPADRTQT----PWTYDPTITDQLHKA 314
            SV G M+  V H T  L   DL A+A YLK+L P   + +    P   D T++      
Sbjct: 251 ASVAGEMSLVVEHSTSHLKREDLQAMAAYLKTLSPVASSGSGRVIPQGVDATVSKLTAAK 310

Query: 315 DLSSRGARIYVDRCAACHRTDGKGYPAVFPPLAGNSVMMQSDPVSLVHIVQKGASLPAMT 374
           DL + G R+Y+D CAACH   G+G P +FP L G +V+   +P +L+H++  GA  P+  
Sbjct: 311 DL-TLGERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAENPSALLHVILAGARTPSTE 369

Query: 375 AAPSSITMPAFSHKLTDQQIADVVTFIRHAWGNNASPVSAEDV 417
            APS + MP F+H+L+D++ A + TF+R  WGN+A  VS  +V
Sbjct: 370 KAPSILVMPGFAHRLSDEEAAALATFVRQGWGNHAGKVSEREV 412


Lambda     K      H
   0.319    0.133    0.420 

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: 587
Number of extensions: 28
Number of successful extensions: 6
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: 437
Length of database: 423
Length adjustment: 32
Effective length of query: 405
Effective length of database: 391
Effective search space:   158355
Effective search space used:   158355
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources