GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Pedobacter sp. GW460-11-11-14-LB5

Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate CA265_RS09620 CA265_RS09620 FAD-binding oxidoreductase

Query= BRENDA::O29853
         (443 letters)



>FitnessBrowser__Pedo557:CA265_RS09620
          Length = 467

 Score =  260 bits (665), Expect = 6e-74
 Identities = 168/448 (37%), Positives = 245/448 (54%), Gaps = 23/448 (5%)

Query: 12  EVFPPSDA---YRFDETPPLVAPRAAENFVVVKPSNSEEVSAILKFANEKSIPVFMRGGG 68
           +VF  +D+   Y  DET  L      +  VVVKP+  EEVSA+LK  N   +PV  RGGG
Sbjct: 22  KVFTDADSLENYSHDETEDL----RYQPEVVVKPTTPEEVSALLKICNAHHVPVTPRGGG 77

Query: 69  TGLSGGAVPTEEGIVLSTEKMTE-LEVDADNRVAICGAGVTLKQLDDAAFRHGLSFPPHP 127
           TGLSG A+P   GI LS EK    L++D +N  A    GV  ++  +A    GL +P  P
Sbjct: 78  TGLSGAALPIYGGISLSMEKFKAILDIDTENLQATVEPGVITEEFINAVAEKGLLYPVDP 137

Query: 128 GAE-TATVGGMIATNAGGVRALKYGTMRNYVLSLEAVLADGRIINVGGKTIKNSSGYSLL 186
            ++ +  +GG +A  +GG R +KYGT+R Y+L+LE VL +G II  G  T+K +SGY+L 
Sbjct: 138 SSKGSCFIGGNVAHGSGGPRVVKYGTIREYILNLEVVLPNGDIIWTGANTLKYASGYNLT 197

Query: 187 HLLVGSEGTLAVITKATIRLFPQMRDMTVLAIPFPTMEDAMNCVVEVARK-MLPMALEFM 245
            L++GSEGTLAV+TK   +L P+     ++   F T EDA   V  + R  + P ALEFM
Sbjct: 198 QLMIGSEGTLAVVTKIVTKLLPKPSQSVLMMGSFSTNEDACAAVSAIFRAGVTPSALEFM 257

Query: 246 EKRAVEIGEKVSGERWVSREGEAHLLMVFESFDEAEEAAK-------IAQSLGAIDVYAA 298
           E++ VE   K    ++  ++  A LLM+    D+ ++  K       + +     +V  A
Sbjct: 258 ERKGVEWVIKFDDIKFDLKDDVAALLMIEFDGDDLDDIFKNCEKTNIVLEEHNCTEVLFA 317

Query: 299 TTKKDQDRLLKVRGMIYEGLR-KEVIEVLDACVPPAKIAEYWRRSNELAEEYGIELITYG 357
            T   ++ L ++R  + E ++   V +  D  VP A + +      E+  +YG E + YG
Sbjct: 318 DTAAQKEELWRMRRTMAESVKSNSVYKEEDTVVPRAALPKLVNGIKEIGAKYGFESVCYG 377

Query: 358 HAGDGNVH----QHPLVYEGWEKSYFEFRKSLLSLAVSLGGVISGEHGIGAVKLSELEEL 413
           HAGDGN+H    +  +  E W+         +  L  +LGG +SGEHGIG V+   +   
Sbjct: 378 HAGDGNLHVNIIKAGMSDEDWKNKLKFGIAEIFELTTALGGTLSGEHGIGLVQKEFMPIK 437

Query: 414 FPE-QFELMRQIKLLFDPKNILNPGKVV 440
           + E    LMR IK +FDPK ILNPGK++
Sbjct: 438 YSEIHLNLMRGIKNIFDPKGILNPGKIM 465


Lambda     K      H
   0.317    0.136    0.388 

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: 502
Number of extensions: 25
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: 443
Length of database: 467
Length adjustment: 33
Effective length of query: 410
Effective length of database: 434
Effective search space:   177940
Effective search space used:   177940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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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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