Aligments for a candidate for gadh1 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh1 in Herbaspirillum seropedicae SmR1

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate HSERO_RS22385 HSERO_RS22385 GMC family oxidoreductase

Query= BRENDA::A4PIB0
         (593 letters)



>FitnessBrowser__HerbieS:HSERO_RS22385
          Length = 593

 Score =  796 bits (2055), Expect = 0.0
 Identities = 376/593 (63%), Positives = 442/593 (74%), Gaps = 1/593 (0%)

Query: 2   MVSRNEKHTDVVIVGFGWVGAIMARELTQAGLNVVALERGPRRDTWPEGAYPSSIDELTH 61
           M ++N K  DVVIVGFGW GAIMA+E+T+AG  VVALERG  RDT+P+GAYP +I+EL +
Sbjct: 1   MANKNMKPVDVVIVGFGWTGAIMAKEMTEAGQRVVALERGVYRDTYPDGAYPKTINELEY 60

Query: 62  NTRHALFLQPSQSTVTVRHRDSDVAAPYRQLAAFLPGTGVGGAGLHWSGCHWRISPVELR 121
             R  LF   ++S+ T R +  D A PYRQ+A F PG GVGGAGLHWSGCHWRI P ELR
Sbjct: 61  QQRFKLFQNLNKSSFTFRRKTGDSAIPYRQIAMFKPGEGVGGAGLHWSGCHWRILPEELR 120

Query: 122 LRSHYEERYGKDFIPQDMTIQDWGVSYEELEPHFAFAESVFGTSGQAYKVNGKIVGD-GN 180
           +RSHYEERYGK+FIP+DMT+QDWGVSYEELEP+F FAE + GTSG AY+V GK+V + GN
Sbjct: 121 MRSHYEERYGKNFIPKDMTLQDWGVSYEELEPYFDFAEKMMGTSGTAYRVGGKVVDESGN 180

Query: 181 PFDADRSTPFPLPAMKNTYSAELYSKAAAECGYHPFRIPSANASQAYTNPYGCQMGACTF 240
           PF+ADRS  FPLPA K  Y A L+ KAA + G HPF +PSANA+  Y N YGCQMG CTF
Sbjct: 181 PFEADRSDNFPLPAQKEQYQAALFRKAAQQAGLHPFTLPSANAAAPYVNQYGCQMGPCTF 240

Query: 241 CGFCSGYACYNYSKASPNVNILPALERESRFELRVECDVLKVETDSSGKKATGVIYRTSK 300
           CGFCSGYACYNYSKASPNVNI+PAL + + FELR  C+VL++E DSS KKATGV Y    
Sbjct: 241 CGFCSGYACYNYSKASPNVNIMPALRQSNLFELRSSCNVLRIELDSSRKKATGVTYVDIN 300

Query: 301 GEEVRQTADIVILASFAYNNPYLLLLSGIGQPYDPKTGEGTVGRNFVYQNESGVTLFFGQ 360
           G+ V Q A IVI ++FAYNN  L LLSGIG+PYDP +  G VGRN  +Q  S +  FF  
Sbjct: 301 GDTVFQPASIVIASTFAYNNARLFLLSGIGKPYDPVSNTGAVGRNIAFQMMSTINAFFEP 360

Query: 361 DKFTNPFIGAGGNGVAIDDFNADNFDHGPLGFVGGAPIWVNQAGSKPISSATVPKGTPQW 420
            K  N FIGAGGNGVA+DDFN D+ DHGPLGFVGG+PIW N +GSKPIS   VP GTP+W
Sbjct: 361 GKNINGFIGAGGNGVAVDDFNGDHMDHGPLGFVGGSPIWCNPSGSKPISGIAVPSGTPRW 420

Query: 421 GAHWKKAVKDSFQHTISIHAHGTNMAFRDCYLSLDPTYSDTAGRPLLRITFNWHDNDVKM 480
           G  WK+AVKDS+ +T+S   HG NM +RD Y+ LDP Y D  G+PLLR TF+W DND++M
Sbjct: 421 GRAWKQAVKDSYLNTMSFDVHGANMVYRDVYVDLDPNYKDAFGQPLLRFTFDWKDNDIRM 480

Query: 481 IRYVTDRMADIGRAMKPESMSVETKEFGEEFDLRHYQTTHIAGGAIMGTSPKDSVVNRYL 540
            RYVTD+   I   +K   + V  K+FG   DLR YQTTH AGG  MGT P  SVVNRYL
Sbjct: 481 SRYVTDQAVKIAHELKAREIKVTVKDFGAAPDLRSYQTTHWAGGVAMGTDPSTSVVNRYL 540

Query: 541 QHWDVSNLFVIGSSAFPQGIGYNPTGIVAALAYWSAKAIRERYLKSPGPMVQA 593
           Q WDV N+F +GS  F QGIGYNPTG   AL YWSA+AIRE+YL  P P+VQA
Sbjct: 541 QSWDVHNVFAVGSGVFAQGIGYNPTGAAVALTYWSARAIREQYLNDPRPLVQA 593


Lambda     K      H
   0.319    0.135    0.423 

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: 1238
Number of extensions: 59
Number of successful extensions: 2
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: 593
Length of database: 593
Length adjustment: 37
Effective length of query: 556
Effective length of database: 556
Effective search space:   309136
Effective search space used:   309136
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 (21.7 bits)
S2: 53 (25.0 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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