GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Nocardiopsis lucentensis DSM 44048

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_017598314.1 D471_RS0108975 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000341125.1:WP_017598314.1
          Length = 904

 Score =  701 bits (1810), Expect = 0.0
 Identities = 381/873 (43%), Positives = 527/873 (60%), Gaps = 63/873 (7%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLTASLKQII-------ESKQELDFPWFPARVVCHDILGQ 89
           +LPY+ +VL ENL+R  +   +TA   + +       +  QE+ F   PARV+  D  G 
Sbjct: 32  RLPYSLKVLLENLLRTEDGANVTADHIRALGEWDAKAQPSQEIQFT--PARVIMQDFTGV 89

Query: 90  TALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRN 149
             +VDLA +R+A+   GGDP ++NP+ P +L++DHS+ V+  G   DAF +N  IE  RN
Sbjct: 90  PCVVDLATMREAVRDLGGDPDKINPLAPAELVIDHSVVVDLFG-RPDAFERNVEIEYERN 148

Query: 150 EDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPH 209
            +R+ F+ W Q AF    V+P G GI+HQ N+E ++ V  +RNG A+PDT VGTDSHT  
Sbjct: 149 YERYKFLRWGQTAFDEFKVVPPGTGIVHQANIEHLARVTMSRNGQAYPDTCVGTDSHTTM 208

Query: 210 VDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRA 269
            + LG++  GVGG+EAE+ MLG+   M +P ++G +L+G+ +PG TATD+VL +TE LR 
Sbjct: 209 QNGLGILGWGVGGIEAEAAMLGQPISMLIPRVVGFKLSGQLKPGTTATDLVLTITEKLRE 268

Query: 270 QKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQV 329
             VV  ++EF+GEG  ++ L +RATI NM+PEFG+TAA+F +D +T+ Y+ LTGR  +QV
Sbjct: 269 HGVVGKFVEFYGEGVSSVPLANRATIGNMSPEFGSTAAIFPVDDETIRYMRLTGRSEQQV 328

Query: 330 KLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV------------- 376
            L E YAK  G W D   +  Y   L  DL+ VV +IAGP  P  R+             
Sbjct: 329 ALTEAYAKANGFWHDPAVEPEYSEYLELDLAEVVPSIAGPKRPQDRIALSEAKPTWRHDV 388

Query: 377 --------------PTSELAARGISGE---------VENEPGLMPDGAVIIAAITSCTNT 413
                         P S+  A   +G           +     +  GAV+IAAITSCTNT
Sbjct: 389 HNYVSDDEAGEESFPASDAPATTANGRPHRPVKVTMADGTETEVDHGAVVIAAITSCTNT 448

Query: 414 SNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVG 473
           SNP  ++ A LLA+ A  KGL+RKPWVKTS+APGSK V  Y E + L P L+ LGF +VG
Sbjct: 449 SNPSVMLGAALLAKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVG 508

Query: 474 FACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAY 533
           + CTTC G SG L   I + V D DL  TAVLSGNRNF+GRI+P  K  +LASPPLVVAY
Sbjct: 509 YGCTTCIGNSGPLPEEISKAVQDNDLAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAY 568

Query: 534 AIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLS 593
           A+AG++  DI  + LG+  DGKPV L +IWPS  EI  V+ A++  + +   Y  +F   
Sbjct: 569 ALAGSLDVDITTEPLGVGSDGKPVYLADIWPSAEEIQEVMDAAIASDMYESAYADVFAGD 628

Query: 594 VDYGDKVSP---LYDWRPQSTYIRRPPYWEGAL---AGERTLKGMRPLAVLGDNITTDHL 647
             +    +P    ++W  +STY+R+PPY+EG     +    + G R LA LGD++TTDH+
Sbjct: 629 ERWRSLPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKLGDSVTTDHI 688

Query: 648 SPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKV 707
           SP+ AI   + A EYL   G+   DFNSY + RG+H    R TFAN +L+N++A      
Sbjct: 689 SPAGAIKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIA----PG 744

Query: 708 KQGSLAR--IEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE 765
            +G   R   +PE  V+ +++A + Y  +  PL+++ G +YG GSSRDWAAKG RL GV 
Sbjct: 745 TEGGYTRDFTQPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVR 804

Query: 766 AIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSI---APRADLTVI 822
           A++ E +ERIHR+NL+GMGVLPL+F  G++  + G+ G E F + G       R   TV 
Sbjct: 805 AVITESYERIHRSNLIGMGVLPLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVK 864

Query: 823 ITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855
           ++   G  VE     R+DT  E   Y  GG+LQ
Sbjct: 865 VSTDTG--VEFDAVVRIDTPGEADYYRNGGILQ 895


Lambda     K      H
   0.318    0.136    0.397 

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: 1966
Number of extensions: 96
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 904
Length adjustment: 43
Effective length of query: 824
Effective length of database: 861
Effective search space:   709464
Effective search space used:   709464
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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