Alignments for a candidate for acnD in Sphingomonas wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Sphingomonas wittichii RW1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_049771290.1 SWIT_RS24185 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000016765.1:WP_049771290.1
          Length = 887

 Score = 1330 bits (3443), Expect = 0.0
 Identities = 664/876 (75%), Positives = 753/876 (85%), Gaps = 12/876 (1%)

Query: 3   TVMNTQ-YRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS 61
           T M +Q +RK LPGTA+DY D R AI+AI PGAY  LPY SRVLAE LVRRC+P +L  +
Sbjct: 11  TAMFSQIFRKKLPGTAVDYHDARAAIDAIRPGAYDGLPYVSRVLAEQLVRRCDPPLLEDA 70

Query: 62  LKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLI 121
           L+QI+E +++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA  GGDPA+VNPVVPTQLI
Sbjct: 71  LRQIVERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEAGGDPARVNPVVPTQLI 130

Query: 122 VDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINL 181
           VDHSLAVE+GGFD  AFAKNRAIEDRRNEDRFHFI WT++AF+N+DVIP GNGIMHQINL
Sbjct: 131 VDHSLAVEHGGFDPQAFAKNRAIEDRRNEDRFHFIEWTRRAFENVDVIPAGNGIMHQINL 190

Query: 182 ERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDI 241
           E+MSPVI  R+GVAFPDT VGTDSHTPHV ALGVIAIGVGGLEAE+VMLGRAS MRLPDI
Sbjct: 191 EKMSPVIQLRDGVAFPDTCVGTDSHTPHVGALGVIAIGVGGLEAETVMLGRASMMRLPDI 250

Query: 242 IGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPE 301
           +GV LTG+  PGITATDIVLALT FLR  +VV +++EFFGEGA AL++GDRATISNM PE
Sbjct: 251 VGVRLTGRRAPGITATDIVLALTAFLREARVVGAWVEFFGEGAAALSIGDRATISNMCPE 310

Query: 302 FGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSS 361
           +GATAAMF+ID QT+DYL LTGR  EQV LVETYAK AGLW+D L+ A Y R L FDLSS
Sbjct: 311 YGATAAMFHIDGQTIDYLRLTGRAPEQVALVETYAKAAGLWADALETAEYERELAFDLSS 370

Query: 362 VVRTIAGPSNPHARVPTSELAARGIS-----GEVENEPGLMPDGAVIIAAITSCTNTSNP 416
           V RT+AGPSNPH R+PTS L  RGI+      + E   GL+PDGAVIIAAITSCTNTSNP
Sbjct: 371 VGRTMAGPSNPHRRLPTSALKERGIATGLVEAQAEERAGLLPDGAVIIAAITSCTNTSNP 430

Query: 417 RNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFAC 476
           RNV+AAGLLA+ AN  GL RKPWVKTS APGS+  +LYLEEA LLPELE+LGFGIVG+AC
Sbjct: 431 RNVVAAGLLAKKANVLGLGRKPWVKTSFAPGSRVARLYLEEAGLLPELEALGFGIVGYAC 490

Query: 477 TTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA 536
           TTCNGMSGALDP I+QE++DRDL+A AVLSGNRNFDGRIHP+A+QAFLASPPLVVAYAIA
Sbjct: 491 TTCNGMSGALDPAIRQEIVDRDLHAVAVLSGNRNFDGRIHPHARQAFLASPPLVVAYAIA 550

Query: 537 GTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDY 596
           GTIRFDIE+DVLG+  DG+ +RL ++WPSD EIDA++AASVKPEQFR+VYEPMF    D 
Sbjct: 551 GTIRFDIEQDVLGV-VDGRDIRLKDLWPSDEEIDAIVAASVKPEQFRRVYEPMFATRSDA 609

Query: 597 GDKVSPLYDWRPQSTYIRRPPYWE----GALAGE-RTLKGMRPLAVLGDNITTDHLSPSN 651
            +   PLYDWRP+STYIRRPPYW+    GALA   R+L GMRPLA+L DN+TTDHLSPSN
Sbjct: 610 AEATPPLYDWRPRSTYIRRPPYWDTEGIGALAASPRSLTGMRPLAILPDNVTTDHLSPSN 669

Query: 652 AIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGS 711
           AI+ +SAAGEYL +MGLPEEDFNSYATHRGDHLTA RATFANP+L NEMA+VDG+V +GS
Sbjct: 670 AILANSAAGEYLARMGLPEEDFNSYATHRGDHLTAMRATFANPQLVNEMAVVDGEVWKGS 729

Query: 712 LARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEG 771
           LAR+EP+G V RMWEAIETY+ R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEG
Sbjct: 730 LARVEPDGTVMRMWEAIETYIGRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEG 789

Query: 772 FERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERV 831
           FERIHRTNL+GMGVLPLEF+ G  R T G+DGTE +DVIG   P A LT+++ R  GE +
Sbjct: 790 FERIHRTNLIGMGVLPLEFRPGTTRLTLGLDGTETYDVIGRRIPGAGLTLLVRRSGGEAI 849

Query: 832 EVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESNLK 867
           EVPV CRLDTAEE SIYEAGGVLQRFAQDFL + ++
Sbjct: 850 EVPVVCRLDTAEEASIYEAGGVLQRFAQDFLAAGVE 885


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: 2284
Number of extensions: 96
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: 867
Length of database: 887
Length adjustment: 42
Effective length of query: 825
Effective length of database: 845
Effective search space:   697125
Effective search space used:   697125
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources