Alignments for a candidate for acnD in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Brevibacterium jeotgali SJ5-8

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_101589524.1 BJEO58_RS11005 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900169175.1:WP_101589524.1
          Length = 894

 Score =  725 bits (1871), Expect = 0.0
 Identities = 396/861 (45%), Positives = 553/861 (64%), Gaps = 50/861 (5%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLTASLKQIIES-------KQELDFPWFPARVVCHDILGQ 89
           KLP++ +VL ENL+R  +   +TA   + + S         E+ F   PARVV  D  G 
Sbjct: 33  KLPFSLKVLLENLLRTEDGANITADHIRTLASWDPTADPSHEIQFT--PARVVMQDFTGV 90

Query: 90  TALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRN 149
             +VDLA +R+A+   GGD  +VNP+ P +L++DHS+ ++  G + +A  +N  IE +RN
Sbjct: 91  PCIVDLATMREAVKELGGDADKVNPLAPAELVIDHSVQIDSFG-NTNAIERNMDIEYQRN 149

Query: 150 EDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR--NGV--AFPDTLVGTDS 205
            +R+ F+ W Q AF +  V+P G GI+HQ+N+E ++ VI  R  +GV  A+PDTLVGTDS
Sbjct: 150 GERYQFLRWGQTAFDDFKVVPPGMGIVHQVNIEYLARVIMPREVDGVLRAYPDTLVGTDS 209

Query: 206 HTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTE 265
           HT  V+ LGV+  GVGG+EAE+ MLG+   M +P ++G +LTG    G+TATD+VL +T+
Sbjct: 210 HTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPPVVGFKLTGGIPSGVTATDVVLTITD 269

Query: 266 FLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGRE 325
            LR   VV  ++EF+G+G  A+ L +RATI NM+PEFG+TAAMF ID+ TLDYL LTGR+
Sbjct: 270 MLRQHGVVGKFVEFYGKGVSAVPLANRATIGNMSPEFGSTAAMFPIDEVTLDYLRLTGRD 329

Query: 326 AEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAARG 385
            +Q+ LVETYAK  GLW D   +  +   L  DLS+VV +I+GP  P  R+  S+  ++ 
Sbjct: 330 EDQMALVETYAKEQGLWHDPEAEIEFSEYLELDLSTVVPSISGPKRPQDRIELSDAKSQ- 388

Query: 386 ISGEVEN--EPG----------------LMPDGAVIIAAITSCTNTSNPRNVIAAGLLAR 427
            + ++ N  +PG                 + +GAV IA+ITSCTNTSNP  ++AAGL+AR
Sbjct: 389 FAKDIHNYAQPGDEQKSAPVATADGREFELTNGAVAIASITSCTNTSNPSVMMAAGLVAR 448

Query: 428 NANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALD 487
            A  KGL+ KPWVKTS+APGSK V  Y E+A L+P+LE+L F IVG+ CTTC G SG L+
Sbjct: 449 KAREKGLSSKPWVKTSIAPGSKVVTEYYEKAGLIPDLEALNFYIVGYGCTTCIGNSGPLE 508

Query: 488 PVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDV 547
             I Q + D DL  +AVLSGNRNF+GRI P  K  +LASPPLV+AYA+AGT+ FD E   
Sbjct: 509 EEISQSIQDNDLSVSAVLSGNRNFEGRISPDVKMNYLASPPLVIAYALAGTMDFDFEGQP 568

Query: 548 LGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LY 604
           LG D DG  V L +IWP+  EI+ +I +S+  + F   Y  +FD    + +  +P   ++
Sbjct: 569 LGQDTDGNDVYLKDIWPAPEEIEELIQSSISTDMFTSEYGTIFDGDHRWKELDTPSGNVF 628

Query: 605 DWRPQSTYIRRPPYWEGALAGERT----LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAG 660
           +W   STY+R+PPY++G +  E T    +KG R LA LGD++TTDH+SP+ +   D+ AG
Sbjct: 629 EWEDSSTYVRKPPYFDG-MTLETTPVEDVKGARVLAKLGDSVTTDHISPAGSFKADTPAG 687

Query: 661 EYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGI 720
            YL + G+  +DFNSY + RG+H    R TFAN +L+N+  ++DG V+ G       EG 
Sbjct: 688 RYLVENGVERKDFNSYGSRRGNHEVMIRGTFANIRLQNQ--LLDG-VQGGFTRDFTQEGA 744

Query: 721 -VTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
             T +++A + Y     PL+++ G +YG GSSRDWAAKG +L GV A++ E FERIHR+N
Sbjct: 745 PQTTIYDASQNYQAAGIPLVVLGGKEYGSGSSRDWAAKGTKLLGVSAVITESFERIHRSN 804

Query: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSI-----APRADLTVIITRKNGERVEVP 834
           L+GMGVLP++F AGE+  + G+DGTE FD+ G          + L V  T+ +G  VE  
Sbjct: 805 LIGMGVLPMQFPAGESAESLGLDGTETFDISGVTKLNEGTTPSTLHVTATKDDGSTVEFD 864

Query: 835 VTCRLDTAEEVSIYEAGGVLQ 855
              R+DT  E   Y  GG+LQ
Sbjct: 865 AVLRIDTPGEADYYRNGGILQ 885


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: 1987
Number of extensions: 95
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 867
Length of database: 894
Length adjustment: 43
Effective length of query: 824
Effective length of database: 851
Effective search space:   701224
Effective search space used:   701224
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 24 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