Alignments for a candidate for acnD in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Dyella japonica UNC79MFTsu3.2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1419
          Length = 916

 Score =  691 bits (1784), Expect = 0.0
 Identities = 381/876 (43%), Positives = 529/876 (60%), Gaps = 64/876 (7%)

Query: 38  LPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDFPWFPARVVCHDILGQTAL 92
           LPY+ ++L ENL+R  +   +TA   + +     +++ + +  + PARVV  D  G   +
Sbjct: 35  LPYSMKILLENLLRHEDGVNVTAKEIEAVARWNPKAEPDTEIAFMPARVVLQDFTGVPCV 94

Query: 93  VDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDR 152
           VDLA +RDA+   GGD  Q+NP+ P +L++DHS+ V+  G  + A  +N AIE +RN++R
Sbjct: 95  VDLAAMRDAVVKLGGDAKQINPLAPAELVIDHSVQVDVYG-SESALEQNVAIEFQRNQER 153

Query: 153 FHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHA--RNGV--AFPDTLVGTDSHTP 208
           + F+ W QKAF N  V+P   GI+HQ+NLE +  V+    ++G   A+PDT+ GTDSHT 
Sbjct: 154 YAFLRWGQKAFDNFKVVPPRTGIVHQVNLEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTT 213

Query: 209 HVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLR 268
            ++ +GV+  GVGG+EAE+ MLG+ S M +P ++G +LTGK   G+TATD+VL +T+ LR
Sbjct: 214 MINGVGVLGWGVGGIEAEAAMLGQPSSMLIPQVVGFKLTGKLAEGVTATDLVLTVTQMLR 273

Query: 269 AQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQ 328
              VV  ++EFFG G + L L DRATI NM PE+GAT  +F +DQ+ L+YL L+GR  E 
Sbjct: 274 KLGVVGKFVEFFGPGLKDLALADRATIGNMAPEYGATCGIFPVDQEALNYLRLSGRSEEH 333

Query: 329 VKLVETYAKTAGLWSDD-LKQAVYPRTLHFDLSSVVRTIAGPSNPHARV----------- 376
           ++LV+ YA+  GLW D+    A +  TL  DL  V  ++AGP  P  RV           
Sbjct: 334 IELVKAYAQAQGLWHDENTPHAQFTTTLELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRD 393

Query: 377 ------------------------------PTSELAARGISGEVENEPGLMPDGAVIIAA 406
                                         P + ++  G+  E   E   + DGAV+IAA
Sbjct: 394 ALGPLTANRRPRNGDTSNFINEGGSAAIGNPANAVSESGVLVEKNGESFRLGDGAVVIAA 453

Query: 407 ITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELES 466
           ITSCTNTSNP  ++ AGLLA+ A AKGL  +PWVKTSL PGSK V  YLE+  LL ELE 
Sbjct: 454 ITSCTNTSNPAVMLGAGLLAKKAAAKGLKAQPWVKTSLGPGSKVVTDYLEKTGLLQELEK 513

Query: 467 LGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLAS 526
           +GF +VG+ CTTC G SG L   I + + + DL   +VLSGNRNF+GR+HP  K  +LAS
Sbjct: 514 VGFYVVGYGCTTCIGNSGPLPAEISKGIAEGDLAVASVLSGNRNFEGRVHPEVKMNYLAS 573

Query: 527 PPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVY 586
           PPLVVAYA+AG++  D+ KD LG   DG+PV L +IWPS+ EI   IA ++ P  F K Y
Sbjct: 574 PPLVVAYALAGSLDVDLSKDPLGTGSDGQPVYLRDIWPSNQEISDTIAGAINPAMFAKNY 633

Query: 587 EPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGD 640
             +F     +    SP   +Y W   STYI+ PPY++G    +     + G R L + GD
Sbjct: 634 ADVFQGDDRWNHIASPDGSVYQW-GDSTYIKNPPYFDGMTREVGKVEDIHGARVLGLFGD 692

Query: 641 NITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM 700
           +ITTDH+SP+ +I  DS AG +L   G+  +DFNSY + RG+     R TFAN +++N M
Sbjct: 693 SITTDHISPAGSIKKDSPAGRFLIGKGVEPKDFNSYGSRRGNDDVMVRGTFANIRIRNLM 752

Query: 701 AIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVR 760
             +DG   +G      P G    +++A   Y     PL+++AG +YG GSSRDWAAKG  
Sbjct: 753 --LDG--VEGGYTLHVPSGEQLAIYDAAMKYKAEHTPLVVLAGKEYGTGSSRDWAAKGTL 808

Query: 761 LAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLT 820
           L GV+A++AE FERIHR+NLVGMGVLP +F+ G++  T G+ G EVFD+ G     + + 
Sbjct: 809 LLGVKAVIAESFERIHRSNLVGMGVLPCQFEDGQSAQTLGLTGKEVFDITGLNDGESKVA 868

Query: 821 -VIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855
            V  T  +G R E  V   L T +E   +  GG+LQ
Sbjct: 869 KVTATAPDGSRKEFIVKVLLLTPKEREFFRHGGILQ 904


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: 2002
Number of extensions: 106
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: 916
Length adjustment: 43
Effective length of query: 824
Effective length of database: 873
Effective search space:   719352
Effective search space used:   719352
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