GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Thiohalospira halophila HL 3

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate WP_093427929.1 BM272_RS06345 FAD-binding protein

Query= BRENDA::Q8N465
         (521 letters)



>NCBI__GCF_900112605.1:WP_093427929.1
          Length = 462

 Score =  203 bits (517), Expect = 1e-56
 Identities = 143/451 (31%), Positives = 213/451 (47%), Gaps = 15/451 (3%)

Query: 76  GGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGM 135
           G ++TDP+       D  R  +G    + +P   ++V+ ILRHCH   + V P+G  TG 
Sbjct: 18  GALLTDPDECWVYGYDNSRR-QGRPVAVAQPEDRDQVAAILRHCHAAGVTVTPRGRGTGT 76

Query: 136 VGGSVPVFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAK 195
            G +VP    +ILST R+ R+    +    +V + G     +     E  F  P D  + 
Sbjct: 77  TGATVPDHGGVILSTERLRRLEPVAADDRYVVAEPGVTNGAVQAAAGEHGFFWPPDPTSA 136

Query: 196 GSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLF 255
             C IGGN+A N+ G R ++YG+     LGLE V  DG VL       K   GYDL +L 
Sbjct: 137 AYCSIGGNLAYNSAGPRAVKYGTPRENTLGLEAVTMDGRVLRSGVRTTKGVVGYDLTRLL 196

Query: 256 IGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDA 315
           IGSEGTL +IT  ++   P P A           A   +  S        +  A EF+D 
Sbjct: 197 IGSEGTLAVITEATLKLTPLPEARATLKAVYADMAAAARAVSRIMAQ-PVVPCALEFIDG 255

Query: 316 VCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEKLGHFLEHALGSGLVTDGTMATD 375
             +++V  H     P + +   ++IE  G  A  +A         A G GL+ D   AT+
Sbjct: 256 AAIEMVHSHSEADLP-EGAGALLMIEVDGPAACLEASATA-VANAAHGEGLL-DLQRATE 312

Query: 376 QRKVKMLWALRERITEALSRDG-YVYKYDLSLPVERLYDIVTDLRARLGPHAKHVVGYGH 434
              V  LWA R+ ++ AL +        D+ +PV R+ +++  L+     H   +V +GH
Sbjct: 313 AADVAALWATRKALSPALRQVAPKKINEDVVVPVSRIPELIEGLQGLGRRHGITIVNFGH 372

Query: 435 LGDGNLHLNVTAEAFSPSLLAALE------PHVYEWTAGQQGSVSAEHGVGFRKRDVLGY 488
            G+GN+H+N+     +P     L+        V+    G  G++S EHGVG  KRD +  
Sbjct: 373 AGNGNIHVNLLV---NPDDAEELDRAWRCLDEVFALVLGLDGTLSGEHGVGLEKRDYVDR 429

Query: 489 SKPPGALQLMQQLKALLDPKGILNPYKTLPS 519
              P  L LM+ +K   DP+G+LNP K LP+
Sbjct: 430 EITPATLDLMRGIKEAFDPRGLLNPGKGLPN 460


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: 618
Number of extensions: 31
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: 462
Length adjustment: 34
Effective length of query: 487
Effective length of database: 428
Effective search space:   208436
Effective search space used:   208436
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 24 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