GapMind for catabolism of small carbon sources

 

Alignments 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.

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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