Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N2C3

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate AO356_02385 AO356_02385 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_02385
          Length = 913

 Score =  729 bits (1882), Expect = 0.0
 Identities = 404/890 (45%), Positives = 547/890 (61%), Gaps = 63/890 (7%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLKQII----ESKQELDF 74
           YF   +A  ++  G   KLP + +VL ENL+R  + + +T A LK +     E + + + 
Sbjct: 22  YFSLPDAARSL--GDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAGWLKERRSDREI 79

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

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

Query: 194 ---VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250
               AFPDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P++IG +L GK 
Sbjct: 199 GRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLIGKL 258

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

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

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

Query: 395 GLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLY 454
             + +GAV+IAAITSCTNTSNP  ++AAGLLA+ A  KGL RKPWVK+SLAPGSK V  Y
Sbjct: 439 HRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLVRKPWVKSSLAPGSKVVTDY 498

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

Query: 515 IHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIA 574
           +HP  K  +LASPPLVVAYA+AGT+R DI  + LG D+DGKPV L +IWPS  E+ A + 
Sbjct: 559 VHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDRDGKPVYLRDIWPSSQEVAAAV- 617

Query: 575 ASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWE---GALAGERT 628
           A V    F K Y  +F     +     P    Y W+  STYI+ PP+++   G     R 
Sbjct: 618 AQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDSTYIQHPPFFDDIGGPPPAVRN 677

Query: 629 LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQR 688
           ++G R LA+LGD++TTDH+SP+  I  DS AG YL + G+   DFNSY + RG+H    R
Sbjct: 678 VEGARVLALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGNHQVMMR 737

Query: 689 ATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQ 748
            TFAN +++NEM  +DG  ++G      P G    +++A   Y     PL++IAG +YG 
Sbjct: 738 GTFANIRIRNEM--LDG--EEGGNTIYIPSGERMPIYDAAMLYQATDTPLVVIAGQEYGT 793

Query: 749 GSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFD 808
           GSSRDWAAKG  L GV+A++AE FERIHR+NLVGMGVLPL+FK  +NR +  + G E  D
Sbjct: 794 GSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGRETLD 853

Query: 809 VIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           ++G     + PR +L ++ITR++G +  + V CR+DT  EV  ++AGG+L
Sbjct: 854 ILGLNDVELTPRMNLPLVITREDGRQERIEVLCRIDTLNEVEYFKAGGIL 903


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: 2032
Number of extensions: 101
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: 1
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, or view the source code.

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