GapMind for catabolism of small carbon sources

 

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

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate CA265_RS09620 CA265_RS09620 FAD-binding oxidoreductase

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__Pedo557:CA265_RS09620
          Length = 467

 Score =  332 bits (851), Expect = 2e-95
 Identities = 176/465 (37%), Positives = 262/465 (56%), Gaps = 3/465 (0%)

Query: 1   MNYKKVEASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKI 60
           MN+ K+    +A IK  + AE+VF   +  E++SHDE   +   PEV++K T+ EEVS +
Sbjct: 1   MNFTKINPEILAEIKAAVGAEKVFTDADSLENYSHDETEDLRYQPEVVVKPTTPEEVSAL 60

Query: 61  MKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLM 120
           +K    H++PV  RG GTGL GA +P++GGI L       IL++DTENL  TVEPGV+  
Sbjct: 61  LKICNAHHVPVTPRGGGTGLSGAALPIYGGISLSMEKFKAILDIDTENLQATVEPGVITE 120

Query: 121 ELSKFVEENDLFYPPDPGEK-SATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEI 179
           E    V E  L YP DP  K S  I GN++  +GG R VKYG  R+Y+  L VVL NG+I
Sbjct: 121 EFINAVAEKGLLYPVDPSSKGSCFIGGNVAHGSGGPRVVKYGTIREYILNLEVVLPNGDI 180

Query: 180 IELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGI 239
           I  G   +K +SGY+L  L+IGSEGTL V+TK + KLLP P  ++ ++  F    DA   
Sbjct: 181 IWTGANTLKYASGYNLTQLMIGSEGTLAVVTKIVTKLLPKPSQSVLMMGSFSTNEDACAA 240

Query: 240 VPKIIKSKAIPTAIEFMERQTILFAEDFLGKKFP-DSSSNAYILLTFDGNTKEQVEAEYE 298
           V  I ++   P+A+EFMER+ + +   F   KF       A +++ FDG+  + +    E
Sbjct: 241 VSAIFRAGVTPSALEFMERKGVEWVIKFDDIKFDLKDDVAALLMIEFDGDDLDDIFKNCE 300

Query: 299 TVANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFI 358
               +       +V   DT  +K+ +W  R    E++K+++   +E D VVPR  + + +
Sbjct: 301 KTNIVLEEHNCTEVLFADTAAQKEELWRMRRTMAESVKSNSVYKEE-DTVVPRAALPKLV 359

Query: 359 EFTHDLAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGL 418
               ++  +       +GHAGDGNLH+ + +  +   DW+ KL   +  ++       G 
Sbjct: 360 NGIKEIGAKYGFESVCYGHAGDGNLHVNIIKAGMSDEDWKNKLKFGIAEIFELTTALGGT 419

Query: 419 VSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           +SGEHGIG  +++++   +   HL LM GIK  FDPK +LNP K+
Sbjct: 420 LSGEHGIGLVQKEFMPIKYSEIHLNLMRGIKNIFDPKGILNPGKI 464


Lambda     K      H
   0.318    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: 550
Number of extensions: 29
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: 466
Length of database: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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