GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Herbaspirillum seropedicae SmR1

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate HSERO_RS19115 HSERO_RS19115 D-lactate dehydrogenase

Query= BRENDA::Q8N465
         (521 letters)



>FitnessBrowser__HerbieS:HSERO_RS19115
          Length = 471

 Score =  178 bits (451), Expect = 4e-49
 Identities = 126/420 (30%), Positives = 200/420 (47%), Gaps = 22/420 (5%)

Query: 108 TSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARMNRVLSFHSVSGILV 167
           ++EEV+  ++ C + +  + P G  T + G  + +   + +  ++MN+VL+ H+      
Sbjct: 60  STEEVAAFVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAVHAEDLTAT 119

Query: 168 CQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLE 227
            QAG   ++L++ +++     P+D GA  S  +GG  +T A G   +RYG++    L L 
Sbjct: 120 VQAGVTRKQLNQEIKDTGLFFPIDPGADAS--LGGMASTRASGTNAVRYGTMKENTLTLT 177

Query: 228 VVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCP 287
           VV A G ++   T  +K + GYDL ++++GSEGTLGIIT V++   P+P A++ A    P
Sbjct: 178 VVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFP 237

Query: 288 GFAEVLQTFSTCKGMLGEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNA 347
             A+ + T      M G  L+  E +D   ++ +  H  L+ PV      +L E  GS  
Sbjct: 238 TVADAVNTVIQTIQM-GVPLARVELLDENGVRAINAHDKLSLPVNP---LLLFEFHGSEN 293

Query: 348 G--HDAEKLGHFLE--HALGSGLVTDGTMATDQRKVKMLWALRERITEALSR---DGYVY 400
           G    AE +    +  HALG         AT       LW  R     AL +        
Sbjct: 294 GVKEQAELVQDIAKEFHALGF------EWATRPEDRTRLWTARHNAYFALLQLRPGARAI 347

Query: 401 KYDLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSLLAALE-- 458
             D  +P+ RL + V   +A            GH+GDGN H+ +  +   P+ +A  E  
Sbjct: 348 STDCCVPISRLAECVLATKADCEEQGLTHAIIGHVGDGNFHVQMMVDPNDPADIARAEGV 407

Query: 459 -PHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517
              +     G  G+ + EHGVG  K D L      GA+ +M+ +K  LDPK I+NP K L
Sbjct: 408 NQRMVARAIGMDGTCTGEHGVGLHKMDFLIQEHGEGAIAVMRAIKHALDPKNIMNPGKIL 467


Lambda     K      H
   0.321    0.139    0.426 

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: 580
Number of extensions: 24
Number of successful extensions: 4
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: 521
Length of database: 471
Length adjustment: 34
Effective length of query: 487
Effective length of database: 437
Effective search space:   212819
Effective search space used:   212819
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.

Links

Downloads

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:

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