Alignments for a candidate for acnD in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Marinobacter adhaerens HP15

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF3491 HP15_3433 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Marino:GFF3491
          Length = 919

 Score =  717 bits (1850), Expect = 0.0
 Identities = 386/916 (42%), Positives = 553/916 (60%), Gaps = 64/916 (6%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRR-----CEPEMLT 59
           +NT       G    Y+   +A + +  G   +LP++ +VL ENL+R       +   + 
Sbjct: 11  LNTLSSLDAGGKTFHYYSLPKAADTL--GDLNRLPFSLKVLMENLLRNEDGTTVDRSHID 68

Query: 60  ASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
           A ++ + +   + +  + PARV+  D  G   +VDLA +R+A+ A G DPA +NP+ P  
Sbjct: 69  AMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSPVD 128

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           L++DHS+ V+  G D  +F  N AIE  RN++R+ F+ W Q+AF N  V+P G GI HQ+
Sbjct: 129 LVIDHSVMVDKFG-DASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQV 187

Query: 180 NLERMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASY 235
           NLE +   +  ++     +A+PDTLVGTDSHT  ++ LG++  GVGG+EAE+ MLG+   
Sbjct: 188 NLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPVS 247

Query: 236 MRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATI 295
           M +P+++G ++TGK + GITATD+VL +TE LR + VV  ++EF+G+G + + + DRATI
Sbjct: 248 MLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRATI 307

Query: 296 SNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTL 355
           +NM PE+GAT   F +D+QT+ Y+ LTGRE EQ++LVE YAK  GLW +   + VY   L
Sbjct: 308 ANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDNL 367

Query: 356 HFDLSSVVRTIAGPSNPHARV------PTSELAARGISGEVEN----------------- 392
             D+  V  ++AGP  P  RV       + EL      G  EN                 
Sbjct: 368 ELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQTAVGVD 427

Query: 393 ---------------EPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRK 437
                          E   +  GAV+IAAITSCTNTSNP  ++AAGL+A+ A  KGL+ K
Sbjct: 428 DSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLSTK 487

Query: 438 PWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDR 497
           PWVKTSLAPGSK V  YL+      +L+ LGF +VG+ CTTC G SG L   +++ + D 
Sbjct: 488 PWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAISDG 547

Query: 498 DLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPV 557
           DL   +VLSGNRNF+GR+HP  K  +LASPPLVVAYA+AG +R D+ +D LG DKDG PV
Sbjct: 548 DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGNPV 607

Query: 558 RLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGD-KV--SPLYDWRPQSTYIR 614
            L ++WPS  EI A     VK + FRK Y  +FD    +   KV  S +Y+W  +STYI+
Sbjct: 608 YLKDLWPSQQEI-AEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYIQ 666

Query: 615 RPPYWEGALAGERT---LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEE 671
            PP++EG          +K    LA+LGD++TTDH+SP+ +   D+ AG+YL + G+  +
Sbjct: 667 HPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEPK 726

Query: 672 DFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETY 731
           DFNSY + RG+H    R TFAN +++NEM  +DG   +G   +  P G    +++A   Y
Sbjct: 727 DFNSYGSRRGNHEVMMRGTFANVRIRNEM--LDG--VEGGYTKFVPTGEQMAIYDAAMKY 782

Query: 732 MDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFK 791
            ++  PL++IAG +YG GSSRDWAAKG RL GV+A+VAE +ERIHR+NL+GMGV+PL+F 
Sbjct: 783 QEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFP 842

Query: 792 AGENRATYGIDGTEVFDV---IGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIY 848
            G +R +  + G E   +    G I P   L + +  K+G      +  R+DTA E   +
Sbjct: 843 EGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYF 902

Query: 849 EAGGVLQRFAQDFLES 864
           + GG+L    ++ L +
Sbjct: 903 KHGGILHYVVREMLRT 918


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: 2007
Number of extensions: 96
Number of successful extensions: 10
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: 919
Length adjustment: 43
Effective length of query: 824
Effective length of database: 876
Effective search space:   721824
Effective search space used:   721824
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