Alignments for a candidate for acnD in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Belnapia rosea CPCC 100156

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_090661743.1 BLR02_RS06435 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900101615.1:WP_090661743.1
          Length = 898

 Score =  711 bits (1835), Expect = 0.0
 Identities = 394/886 (44%), Positives = 538/886 (60%), Gaps = 43/886 (4%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           + T+    + G    YF   EA  +I  G  A+LPY+ +VL EN++R  +    T    +
Sbjct: 9   LKTRRTLEVDGKTYHYFSLPEAARSI--GDIARLPYSLKVLLENILRYEDGRSYTVDDAK 66

Query: 65  II-----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
            I         + + P+ P+R++  D  G  A+VDLA +RD I A GGDP +VNP+VP  
Sbjct: 67  SIAGWLPSGHSDKEVPFRPSRILMQDFTGVPAVVDLAAMRDGIIALGGDPRKVNPLVPVD 126

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           L++DHS+ V+  G  + A  +N  IE +RN +R+ F+ W Q AF N  V+P G GI HQ+
Sbjct: 127 LVIDHSVMVDVSGTPQ-ALQRNVDIEFQRNGERYEFLRWGQAAFDNFRVVPPGTGICHQV 185

Query: 180 NLERMSPVIHARNGVA----FPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASY 235
           NLE ++ V      +     +PD+  GTDSHT  V+ LGV+  GVGG+EAE+ MLG+   
Sbjct: 186 NLEYLAQVAWTSQDIGDTYVYPDSCYGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPIA 245

Query: 236 MRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATI 295
           M +PD+IG +LTGK + G+TATD+VL +T+ LR + VV  ++EFFG G + L L DRATI
Sbjct: 246 MLIPDVIGFKLTGKLREGVTATDLVLTVTQMLRKKGVVGKFVEFFGPGLDDLPLADRATI 305

Query: 296 SNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLK-QAVYPRT 354
            NM PE+GAT   F +D  T+ YL L+GRE  ++KLVE YAK  G+W D      V+  T
Sbjct: 306 GNMAPEYGATCGFFPVDAVTIGYLRLSGREEHRIKLVEAYAKAQGMWRDSSSPDPVFTDT 365

Query: 355 LHFDLSSVVRTIAGPSNPHARVPTSELAAR----------GISGE-------VENEPGLM 397
           L  D+++V  ++AGP  P  RV  S  A            G+ G+       VE     +
Sbjct: 366 LELDMATVEPSLAGPKRPQDRVALSNAATSFAKDLAAGTMGVPGDEATKRVPVEGANYDL 425

Query: 398 PDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEE 457
             G V+IAAITSCTNTSNP  ++AAGL+AR A  KGL  KPWVKTSLAPGS+ V  Y E+
Sbjct: 426 GHGDVVIAAITSCTNTSNPYVMVAAGLVARKAREKGLAPKPWVKTSLAPGSQVVTEYFEK 485

Query: 458 ANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHP 517
           + L  +L+++GF  VG+ CTTC G SG L   I   + +  L A +VLSGNRNF+GR+H 
Sbjct: 486 SGLQADLDAIGFQTVGYGCTTCIGNSGPLPDPIVDAIENNKLVAASVLSGNRNFEGRVHA 545

Query: 518 YAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASV 577
             +  +LASPPLVVAYA+AGTI  DI K+ +G   DG+PV L +IWP+  E++  + A V
Sbjct: 546 NVRANYLASPPLVVAYALAGTITKDITKEPIGTGSDGQPVYLKDIWPTQKEVNDTVHACV 605

Query: 578 KPEQFRKVYEPMFDLSVDYG----DKVSPLYDWRPQSTYIRRPPYWEGALAGER---TLK 630
             E F+  Y  +F     +     D  S  Y W   STY++ PPY+EG  A  +   ++ 
Sbjct: 606 TREMFQGRYGDVFKGPEQWQAIRVDADSDTYRWNSGSTYVQNPPYFEGMSADIKPVTSVH 665

Query: 631 GMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRAT 690
           G R LA L D+ITTDH+SP+  I   S AGEYL +  + ++DFNSY   RG+H    R T
Sbjct: 666 GARVLAELADSITTDHISPAGNIRKASPAGEYLVEHQVRQDDFNSYGARRGNHEVMMRGT 725

Query: 691 FANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGS 750
           FAN ++KNEM  V G   +G +++  P G V  ++     Y     PL++  G +YG GS
Sbjct: 726 FANIRIKNEM--VPG--TEGGISKHYPSGDVAPIYNVAMRYKAEGVPLVVFGGKEYGTGS 781

Query: 751 SRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVI 810
           SRDWAAKG  L GV+A++AE FERIHR+NLVGMGVLPL F  GE+R + GI G EV D++
Sbjct: 782 SRDWAAKGTFLLGVKAVIAESFERIHRSNLVGMGVLPLVFMNGEDRKSLGIQGDEVIDIL 841

Query: 811 G--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           G   ++PR  L ++I R +G      V  R+DTA+EV  Y+ GG+L
Sbjct: 842 GLEQLSPRQTLELVIRRADGTETRTKVLSRIDTADEVEYYKNGGIL 887


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: 1976
Number of extensions: 101
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: 898
Length adjustment: 43
Effective length of query: 824
Effective length of database: 855
Effective search space:   704520
Effective search space used:   704520
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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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