Alignments for a candidate for acnD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas fluorescens GW456-L13

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate PfGW456L13_4052 Aconitate hydratase (EC 4.2.1.3)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052
          Length = 913

 Score =  719 bits (1856), Expect = 0.0
 Identities = 406/916 (44%), Positives = 561/916 (61%), Gaps = 65/916 (7%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLK 63
           +NT     +      YF   EA +++  G   KLP + +VL ENL+R  + + +T A LK
Sbjct: 7   LNTLKTLQVGNKTYHYFSLPEAAKSL--GDLNKLPMSLKVLLENLLRWEDEKTVTGADLK 64

Query: 64  QII----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
            +     E + + +  + PARV+  D  G  A+VDLA +R A+A  GG+P ++NP+ P  
Sbjct: 65  ALAAWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGNPQRINPLSPVD 124

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           L++DHS+ V+       AF +N  IE +RN +R+ F+ W Q AF N  V+P G GI HQ+
Sbjct: 125 LVIDHSVMVDKFA-SSSAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQV 183

Query: 180 NLERMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASY 235
           NLE +   +  ++      AFPDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   
Sbjct: 184 NLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 243

Query: 236 MRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATI 295
           M +P++IG +LTGK + GITATD+VL +T+ LR + VV  ++EF+G+G   L L DRATI
Sbjct: 244 MLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATI 303

Query: 296 SNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTL 355
           +NM PE+GAT   F +D  TLDYL L+GR  E V+LVE Y+K  GLW    ++ V+  +L
Sbjct: 304 ANMAPEYGATCGFFPVDDITLDYLRLSGRPLETVQLVEAYSKAQGLWRLPGQEPVFTDSL 363

Query: 356 HFDLSSVVRTIAGPSNPHARV------------------PTSELAAR------------- 384
             D+ SV   +AGP  P  RV                  PTS+   R             
Sbjct: 364 ALDMGSVEACLAGPKRPQDRVTLPNVAQAFSDFTDLQFKPTSKEEGRLESEGGGGVAVGN 423

Query: 385 -GISGEV----ENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPW 439
             ++GE     E +   + +GAV+IAAITSCTNTSNP  ++AAGL+A+ A  KGL RKPW
Sbjct: 424 ADMAGEADYDYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPW 483

Query: 440 VKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDL 499
           VK+SLAPGSK V  Y + A L   L+ LGF +VG+ CTTC G SG L   I++ +   DL
Sbjct: 484 VKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLSEPIEKAIQQADL 543

Query: 500 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRL 559
              +VLSGNRNF+GR+HP  K  +LASPPLVVAYA+AGT+R D+ ++ LG  KDGKPV L
Sbjct: 544 TVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRTDLSREPLGDGKDGKPVYL 603

Query: 560 INIWPSDAEI-DAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRR 615
            +IWPS  EI DAV    V    F K Y  +F     +     P    Y W+  STYI+ 
Sbjct: 604 RDIWPSSKEIADAV--NQVNTAMFHKEYAEVFAGDEQWQAIKVPQAATYVWQDDSTYIQH 661

Query: 616 PPYWE---GALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEED 672
           PP+++   G     + + G R LA+LGD++TTDH+SP+  I +DS AG+YL   G+   D
Sbjct: 662 PPFFDDIGGPAPVVKDVSGARILALLGDSVTTDHISPAGNIKVDSPAGQYLRDKGVEPRD 721

Query: 673 FNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYM 732
           FNSY + RG+H    R TFAN +++NEM  + G  ++G   R  P G    +++A   Y 
Sbjct: 722 FNSYGSRRGNHEVMMRGTFANIRIRNEM--LGG--EEGGNTRYIPTGEKMSIYDAAMRYQ 777

Query: 733 DRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKA 792
               PL++IAG +YG GSSRDWAAKG  L GV+A+VAE FERIHR+NLVGMGVLPL+FK 
Sbjct: 778 ASGTPLVVIAGQEYGTGSSRDWAAKGTILLGVKAVVAESFERIHRSNLVGMGVLPLQFKL 837

Query: 793 GENRATYGIDGTEVFDVIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIY 848
            +NR +  + G+E  D++G     + PR +LT++ITR++G R ++ V CR+DT  EV  +
Sbjct: 838 DQNRKSLKLGGSETLDILGLTGVELTPRMNLTLVITREDGSREKIEVLCRIDTLNEVEYF 897

Query: 849 EAGGVLQRFAQDFLES 864
           ++GG+L    +  + S
Sbjct: 898 KSGGILHYVLRQLIAS 913


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: 1991
Number of extensions: 95
Number of successful extensions: 9
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: 913
Length adjustment: 43
Effective length of query: 824
Effective length of database: 870
Effective search space:   716880
Effective search space used:   716880
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 17 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