Alignments for a candidate for acnD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas simiae WCS417

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF1478 PS417_07515 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__WCS417:GFF1478
          Length = 913

 Score =  724 bits (1869), Expect = 0.0
 Identities = 409/901 (45%), Positives = 557/901 (61%), Gaps = 65/901 (7%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLKQII----ESKQELDF 74
           YF   EA +++  G   KLP + +VL ENL+R  + + +T A LK I     E + + + 
Sbjct: 22  YFSLPEAAKSL--GDLDKLPMSLKVLLENLLRWEDNKTVTGADLKAIAAWLKERQSDREI 79

Query: 75  PWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFD 134
            + PARV+  D  G  A+VDLA +R A+A  GGDP ++NP+ P  L++DHS+ V+  G  
Sbjct: 80  QYRPARVLMQDFTGVPAVVDLAAMRAAVAKAGGDPQRINPLSPVDLVIDHSVMVDKFG-T 138

Query: 135 KDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG- 193
             AF +N  IE +RN +R+ F+ W Q AF N  V+P G GI HQ+NLE +   +  ++  
Sbjct: 139 TGAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKDED 198

Query: 194 ---VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250
               AFPDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P++IG +LTGK 
Sbjct: 199 GRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKL 258

Query: 251 QPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFY 310
           + GITATD+VL +T+ LR + VV  ++EF+G+G   L L DRATI+NM PE+GAT   F 
Sbjct: 259 KEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFP 318

Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370
           +D+ TLDYL L+GR  E VKLVE Y K  GLW +  ++ V+  +L  D+ SV  ++AGP 
Sbjct: 319 VDEVTLDYLRLSGRPTETVKLVEAYTKAQGLWRNAGQEPVFTDSLALDMGSVEASLAGPK 378

Query: 371 NPHARV------------------PTSE----LAARGISG--------------EVENEP 394
            P  RV                  PT++    L + G  G              E + + 
Sbjct: 379 RPQDRVALPNVGQAFSDFLDLQFKPTNKEEGRLESEGGGGVAVGNADLVGETDYEYDGQT 438

Query: 395 GLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLY 454
             + +GAV+IAAITSCTNTSNP  ++AAGLLA+ A  KGLTRKPWVKTSLAPGSK V  Y
Sbjct: 439 YRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLTRKPWVKTSLAPGSKVVTDY 498

Query: 455 LEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGR 514
            + A L   L+ LGF +VG+ CTTC G SG L   I++ +   DL   +VLSGNRNF+GR
Sbjct: 499 YKAAGLTQYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQKADLAVASVLSGNRNFEGR 558

Query: 515 IHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEI-DAVI 573
           +HP  K  +LASPPLVVAYA+AGT+R DI  + LG D+ G PV L +IWP+  EI DAV 
Sbjct: 559 VHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDQHGHPVYLKDIWPTSQEIADAV- 617

Query: 574 AASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWE---GALAGER 627
            A V    F K Y  +F     +     P    Y W+  STYI+ PP+++   G L   +
Sbjct: 618 -AQVTTGMFHKEYAEVFAGDEQWQAIEVPQAATYVWQKDSTYIQHPPFFDDIAGPLPVIK 676

Query: 628 TLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQ 687
            +KG   LA+LGD++TTDH+SP+  I  DS AG YL + G+   DFNSY + RG+H    
Sbjct: 677 DVKGANVLALLGDSVTTDHISPAGNIKTDSPAGRYLREQGVEPRDFNSYGSRRGNHEVMM 736

Query: 688 RATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYG 747
           R TFAN +++NEM    G  + G+   I P G    +++A   Y     PL+++AG +YG
Sbjct: 737 RGTFANIRIRNEML---GGEEGGNTLYI-PTGEKMPIYDASMKYQASGTPLVVVAGQEYG 792

Query: 748 QGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVF 807
            GSSRDWAAKG  L GV+A++AE FERIHR+NLVGMGVLPL+FK  +NR +  + G E  
Sbjct: 793 TGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLKLTGKEKI 852

Query: 808 DVIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863
           D++G     I PR +LT++ITR++G   +V V CR+DT  EV  +++GG+L    +  + 
Sbjct: 853 DILGLTDVEIVPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKSGGILHYVLRQLIA 912

Query: 864 S 864
           S
Sbjct: 913 S 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: 2028
Number of extensions: 90
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