Alignments for a candidate for acnD in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudarthrobacter sulfonivorans Ar51

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_058929322.1 AU252_RS02190 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001484605.1:WP_058929322.1
          Length = 936

 Score =  697 bits (1800), Expect = 0.0
 Identities = 394/900 (43%), Positives = 539/900 (59%), Gaps = 88/900 (9%)

Query: 38  LPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDFPWFPARVVCHDILGQTAL 92
           LP++ +VL ENL+R  +   +TA   + +     +++   +  + PARV+  D  G   +
Sbjct: 34  LPFSLKVLLENLLRTEDGANITADHVRALAGWDPDAQPNTEIQFTPARVIMQDFTGVPCV 93

Query: 93  VDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDR 152
           VDLA +R+A+   GGDP +VNP+ P ++++DHS+ ++  G +  A  +N  IE +RN +R
Sbjct: 94  VDLATMREAVKELGGDPKRVNPLAPAEMVIDHSVQIDAFG-NSGALERNMEIEYQRNGER 152

Query: 153 FHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR--NGV--AFPDTLVGTDSHTP 208
           + F+ W Q AF +  V+P G GI+HQ+N+E ++  +  R  +GV  A+PDT VGTDSHT 
Sbjct: 153 YQFLRWGQTAFDDFKVVPPGTGIVHQVNIEYLARTVMTREIDGVLRAYPDTCVGTDSHTT 212

Query: 209 HVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLR 268
            V+ LGV+  GVGG+EAE+ MLG+   M +P ++G +LTG    G TATD+VL +TE LR
Sbjct: 213 MVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRVVGFKLTGSIPAGATATDVVLTITEQLR 272

Query: 269 AQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQ 328
              VV  ++EF+GEG  A+ L +RATI NM+PEFG+TAAMF ID  TLDYL LTGR  E 
Sbjct: 273 KHGVVGKFVEFYGEGVAAVPLANRATIGNMSPEFGSTAAMFPIDDVTLDYLRLTGRSDEN 332

Query: 329 VKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV------------ 376
           V LVE+YAK  GLW D  ++  +   L  DLS+VV +I+GP  P  R+            
Sbjct: 333 VALVESYAKEQGLWHDASREIKFSEYLELDLSTVVPSISGPKRPQDRIELTDAKEQFRKD 392

Query: 377 --------------------PTSEL------------------AARGISGEVENEPGLMP 398
                               P S+                   AA G  G   N   +  
Sbjct: 393 IHNYVAIEDGSVDESLDESFPASDAPSFTHADSHTTETSRVVSAANGAHGRPSNPVHIKT 452

Query: 399 D---------GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSK 449
           +         GAV IA+ITSCTNTSNP  ++AA LLARNA  KGLT KPWVKTS+APGSK
Sbjct: 453 EDGREFELDHGAVSIASITSCTNTSNPSVMLAAALLARNAVDKGLTSKPWVKTSVAPGSK 512

Query: 450 AVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNR 509
            V  Y  ++ L P LE LGF IVG+ C TC G SG LD  I + +   DL  TAVLSGNR
Sbjct: 513 VVTDYYNKSGLTPYLEKLGFYIVGYGCATCIGNSGPLDAEISEAIQANDLSVTAVLSGNR 572

Query: 510 NFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEI 569
           NF+GRI+P  K  +LASPPLV+AYA+AG++ FD + D LG D+ G  V L +IWP+  E+
Sbjct: 573 NFEGRINPDVKMNYLASPPLVIAYALAGSMDFDFDTDSLGKDEAGNDVFLKDIWPNPVEV 632

Query: 570 DAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLYD---WRPQSTYIRRPPYWEGALAGE 626
             VI +S+  + F + YE +FD    +    +P  D   W P STY+R+PPY++G  A  
Sbjct: 633 QQVIDSSIDKDMFARGYEGVFDGDARWKALDTPAGDTFAWDPNSTYVRKPPYFDGIKAQP 692

Query: 627 ---RTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDH 683
              + + G R L  LGD++TTDH+SP+ +   D+ AG+YL   G+  +DFNSY + RG+H
Sbjct: 693 EPVQDISGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNH 752

Query: 684 LTAQRATFANPKLKNEMAIVDGKVKQGSLAR--IEPEGIVTRMWEAIETYMDRKQPLIII 741
               R TFAN ++KN+  I+DG   +G   R   + +G    +++A + Y     PL+++
Sbjct: 753 EVMIRGTFANIRIKNQ--ILDG--VEGGFTRDFTQADGPQAYVYDAAQNYQAAGTPLVVL 808

Query: 742 AGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGI 801
           AG +YG GSSRDWAAKG  L GV+A+VAE +ERIHR+NL+GMGVLPL+F AGE+ AT G+
Sbjct: 809 AGKEYGSGSSRDWAAKGTALLGVKAVVAESYERIHRSNLIGMGVLPLQFPAGESAATLGL 868

Query: 802 DGTEVFDVIGSIA------PRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855
            GTE F V G  A      P+  L V  T ++G         R+DT  E   Y  GG+LQ
Sbjct: 869 TGTETFAVEGVTALNEGTTPKT-LKVTATAEDGSAKSFDAVLRIDTPGEADYYRNGGILQ 927


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: 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: 936
Length adjustment: 43
Effective length of query: 824
Effective length of database: 893
Effective search space:   735832
Effective search space used:   735832
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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 2024 update 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