Alignments for a candidate for acnD in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Dinoroseobacter shibae DFL-12

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 3608455 Dshi_1851 aconitate hydratase 1 (RefSeq)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Dino:3608455
          Length = 928

 Score =  683 bits (1762), Expect = 0.0
 Identities = 383/893 (42%), Positives = 527/893 (59%), Gaps = 73/893 (8%)

Query: 26  AIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIE--------SKQELDFPWF 77
           A E    G ++KLP   +V+ EN++R  E    T S+  I           +   +  + 
Sbjct: 30  AAETAGLGDFSKLPAALKVVLENMLR-FEDGGRTVSVDDIRAFADWADKGGQNPREIAYR 88

Query: 78  PARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDA 137
           PARV+  D  G  A+VDLA +RD I   GGD  ++NP+ P  L++DHS+ ++  G  + A
Sbjct: 89  PARVLMQDFTGVPAVVDLAAMRDGIVGLGGDAEKINPLNPVDLVIDHSVMIDEFGNPR-A 147

Query: 138 FAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVI-----HARN 192
           F  N   E  RN +R+ F+ W Q AF N  V+P G GI HQ+NLE ++  +      +  
Sbjct: 148 FQMNVDREYERNIERYTFLKWGQSAFANFRVVPPGTGICHQVNLEYLAQAVWTDTDQSGQ 207

Query: 193 GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQP 252
            VA+PDTLVGTDSHT  V+ + V+  GVGG+EAE+ MLG+   M +P+++G ELTG+   
Sbjct: 208 EVAYPDTLVGTDSHTTMVNGMAVLGWGVGGIEAEAAMLGQPISMLIPEVVGFELTGEMME 267

Query: 253 GITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYID 312
           G T TD+VL + E LRA+ VV  ++EF+G G + L L DRATI+NM PE+GAT   F ID
Sbjct: 268 GTTGTDLVLKVVEMLRAKGVVGKFVEFYGAGLDHLPLADRATIANMAPEYGATCGFFPID 327

Query: 313 QQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNP 372
            +TL Y+  TGR+  ++ LVE YAK  GLW  D    VY  TL  D+ ++V  I+GP  P
Sbjct: 328 GETLRYMRTTGRDEARIALVEAYAKENGLWRGDDYAPVYTDTLSLDMGTIVPAISGPKRP 387

Query: 373 HARVPTSE--------------------------------LAARGISGE--------VEN 392
              V   +                                +A R I G+        V  
Sbjct: 388 QDYVALDKAAETFRDYVTGQRPDWSADEEDKAEWTDEGGAVAPRDIPGDRGKHKRARVRG 447

Query: 393 EPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQ 452
               + DG ++IA+ITSCTNTSNP  +I AGL+AR A A GLTRKPWVKTSLAPGS+ V 
Sbjct: 448 ADYTIHDGTIVIASITSCTNTSNPYVMIGAGLVARKARALGLTRKPWVKTSLAPGSQVVS 507

Query: 453 LYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFD 512
            YLE A L  +L+++GF +VG+ CTTC G SG +   + + + D D+ AT+VLSGNRNF+
Sbjct: 508 AYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSGPIQEELSEAINDGDIIATSVLSGNRNFE 567

Query: 513 GRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAV 572
           GRI P  +  +LASPPLVVAYA+AG +  D+ +D LG D+DG  V L +IWPS  EI  +
Sbjct: 568 GRISPDVRANYLASPPLVVAYALAGDMNVDLTRDPLGQDRDGNDVYLKDIWPSTKEIAEL 627

Query: 573 IAASVKPEQFRKVYEPMFD-----LSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGER 627
           +  +V  E F+  Y  +F       SV+  D ++  YDW P STY++ PPY++G  A   
Sbjct: 628 VEQTVTREAFQAKYADVFKGDEKWQSVETTDSLT--YDWPPSSTYVQNPPYFQGMSAEPG 685

Query: 628 T---LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHL 684
           T   ++G + LA+LGD ITTDH+SP+ +    + AG YL +  +   +FNSY + RG+H 
Sbjct: 686 TISNIEGAKILAILGDMITTDHISPAGSFKESTPAGRYLTERQVQPREFNSYGSRRGNHE 745

Query: 685 TAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGA 744
              R TFAN +++NEM  +DG V+ G    + P+G  T ++EA   Y +   PL+I  G 
Sbjct: 746 VMMRGTFANIRIRNEM--LDG-VEGG--YTLGPDGQQTSIFEAAMAYQEMGTPLVIFGGE 800

Query: 745 DYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGT 804
            YG GSSRDWAAKG  L GV+A++AE FERIHR+NLVGMGV+P EF  G+ R T G+ G 
Sbjct: 801 QYGAGSSRDWAAKGTSLLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKTLGLKGD 860

Query: 805 EVFDVI---GSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           E   +    G I P +++   IT  +G   E+ + CR+DT  E+   E GGVL
Sbjct: 861 ETVSITGLDGKIVPLSEMPCTITYGDGTTREITLKCRIDTEVEIEYIENGGVL 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: 2072
Number of extensions: 113
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: 928
Length adjustment: 43
Effective length of query: 824
Effective length of database: 885
Effective search space:   729240
Effective search space used:   729240
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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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