Alignments for a candidate for acnD in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Azospirillum brasilense Sp245

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__azobra:AZOBR_RS02985
          Length = 896

 Score =  731 bits (1886), Expect = 0.0
 Identities = 396/884 (44%), Positives = 552/884 (62%), Gaps = 40/884 (4%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVR-----RCEPEMLT 59
           + T+    + G + DYF  + A +A   G  ++LPY+ +VL ENL+R         + + 
Sbjct: 10  LKTRRSLSVGGKSYDYFSIKAAEDA-GLGDLSRLPYSMKVLLENLLRFEDGRTVSTDDVK 68

Query: 60  ASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
           A  + + + + + +  + PARV+  D  G  A+ DLA +R+A+AA GGDP ++NP+VP  
Sbjct: 69  AVAQWLHDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLVPVD 128

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           L++DHS+ V+Y G +  AF KN  +E  RN +R+ F+ W QKAF N  V+P G GI HQ+
Sbjct: 129 LVIDHSVMVDYFG-NPSAFEKNVELEFERNLERYAFLRWGQKAFDNFRVVPPGTGICHQV 187

Query: 180 NLERMSPVIH-----ARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS 234
           N+E ++  +      A   VA+PDTLVGTDSHT  V+ LGV+  GVGG+EAE+ MLG+  
Sbjct: 188 NVEYLAQGVWTDTDPAGKLVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPI 247

Query: 235 YMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRAT 294
            M +P+++G +LTG+ + G TATD+VL +T+ LR + VV  ++EF+G G + LTL DRAT
Sbjct: 248 SMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGLDHLTLADRAT 307

Query: 295 ISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-DLKQAVYPR 353
           I NM PE+GAT  +F ID +T+ YLT TGR+A++V +VE YA+  G+W D      V+  
Sbjct: 308 IGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDAGTPDPVFTD 367

Query: 354 TLHFDLSSVVRTIAGPSNPHARVPTSELA---ARGISGEVENEPG-----------LMPD 399
            L  D+++V  ++AGP  P  RVP S+ A      + G  + E              +  
Sbjct: 368 ALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAEDADRSVPVKGCGYNLDQ 427

Query: 400 GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEAN 459
           GAV+IAAITSCTNTSNP  ++AAGLLAR A  KGL  KPWVKTSLAPGS+ V  YL +A 
Sbjct: 428 GAVVIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAKAG 487

Query: 460 LLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYA 519
           L P L+ LGF IVG+ CTTC G SG L   I   V + +L   AVLSGNRNF+GR++P+ 
Sbjct: 488 LQPYLDQLGFNIVGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNPHT 547

Query: 520 KQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKP 579
           +  +LASPPL VAYA+AG ++ D+ KD +G   DG+PV L ++WP++ E+   I AS+  
Sbjct: 548 RANYLASPPLCVAYALAGNMKIDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASLSA 607

Query: 580 EQFRKVYEPMFDLSVDY---GDKVSPLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMR 633
           E FR  Y  +F+    +          Y+W+  STY++ PP++            ++G R
Sbjct: 608 EMFRSRYGNVFEGPEQWRGIQTAEGQTYEWQAGSTYVKLPPFFADMPKTPDAVSDVRGAR 667

Query: 634 PLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFAN 693
            LAVLGD+ITTDH+SP+ +I   S AGEYL    +  +DFNSY   RG+H    R TFAN
Sbjct: 668 ALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQDFNSYGARRGNHEVMMRGTFAN 727

Query: 694 PKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRD 753
            +++NEM        +G   R  P G    ++ A   Y     PL++IAG +YG GSSRD
Sbjct: 728 IRIRNEML----AGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKEYGTGSSRD 783

Query: 754 WAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG-- 811
           WAAKG +L G+ A++AE FERIHR+NLVGMG+LPL+FK G  R    +DGTE FD+ G  
Sbjct: 784 WAAKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIE 843

Query: 812 -SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
             + PR D+T+ ITR +G+  +VP+  R+DT +EV  Y  GGVL
Sbjct: 844 QDLRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVL 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: 1991
Number of extensions: 101
Number of successful extensions: 10
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: 896
Length adjustment: 43
Effective length of query: 824
Effective length of database: 853
Effective search space:   702872
Effective search space used:   702872
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