Alignments for a candidate for acnD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas stutzeri RCH2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF2473 Psest_2521 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__psRCH2:GFF2473
          Length = 891

 Score =  716 bits (1847), Expect = 0.0
 Identities = 400/877 (45%), Positives = 538/877 (61%), Gaps = 49/877 (5%)

Query: 15  GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LKQIIE----SK 69
           G    Y+   +A   +  G  ++LP + +VL ENL+R  + + + A  LK ++       
Sbjct: 17  GKTYHYYSLPDAAAQL--GDISRLPTSLKVLLENLLRWEDNQTVRADDLKSLVSWLDTRS 74

Query: 70  QELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVE 129
             ++  + PARV+  D  G  A+VDLA +RDA+A  GGDP ++NP+ P  L++DHS+ V+
Sbjct: 75  STMEIQYRPARVLMQDFTGVPAVVDLAAMRDAVAKAGGDPQKINPLSPVDLVIDHSVMVD 134

Query: 130 YGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIH 189
             G D+ AF +N  IE +RN +R+ F+ W Q+AF N  V+P G GI HQ+NLE +  V+ 
Sbjct: 135 RFGSDQ-AFEQNVEIEMQRNGERYEFLRWGQQAFDNFAVVPPGTGICHQVNLEYLGQVVW 193

Query: 190 AR--NG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVE 245
            R  NG   A+PDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P++IG  
Sbjct: 194 TREENGETFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFR 253

Query: 246 LTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGAT 305
           LTGK   G+TATD+VL +T+ LR   VV  ++EF+G G + L L DRATI NM PE+GAT
Sbjct: 254 LTGKLNEGVTATDLVLTVTQMLRKHGVVGKFVEFYGPGLDHLPLADRATIGNMAPEYGAT 313

Query: 306 AAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVR 364
              F +DQ T+DYL LTGR  E++ LVE Y+K  G+W D    A  +  TL  DLS V  
Sbjct: 314 CGFFPVDQVTIDYLRLTGRNEERIALVEAYSKAQGMWRDSNSPAPEFTATLELDLSQVRP 373

Query: 365 TIAGPSNPHARVPTSELAAR-----GISGE---------VENEPGLMPDGAVIIAAITSC 410
           ++AGP  P  RV   ++ A        SG          V  E   +  GAV+IAAITSC
Sbjct: 374 SVAGPKRPQDRVTLGDIGANFDLLLETSGRQQQADTDFAVAAEQFQLKHGAVVIAAITSC 433

Query: 411 TNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFG 470
           TNTSNP  ++AAGL+A+ A  +GL RKPWVKTSLAPGSK V  YLE A L   L+ LGF 
Sbjct: 434 TNTSNPNVLMAAGLVAKKAIERGLQRKPWVKTSLAPGSKVVTDYLERAGLTRYLDELGFN 493

Query: 471 IVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLV 530
           +VG+ CTTC G SG L   I Q + D DL  ++VLSGNRNF+GR+HP  K  +LASPPLV
Sbjct: 494 LVGYGCTTCIGNSGPLPDAIGQAITDNDLIVSSVLSGNRNFEGRVHPLVKANWLASPPLV 553

Query: 531 VAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF 590
           VA+A+AGT R D++++ LG D   +PV L +IWPS AEI A   A +  E FR  Y  +F
Sbjct: 554 VAFALAGTTRIDMDREPLGYDAQNQPVYLKDIWPSSAEI-AEAVARIDGEMFRSRYADVF 612

Query: 591 D-------LSVDYGDKVSPLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGD 640
                   + V  GD     Y W   S+Y++ PPY+E           ++  R LAV GD
Sbjct: 613 SGDEHWQKIPVSAGD----TYAWNANSSYVQNPPYFEDIGQPPTPPADVENARVLAVFGD 668

Query: 641 NITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM 700
           +ITTDH+SP+  I   S AG YL  +G+  EDFNSY + RG+H    R TFAN +++NEM
Sbjct: 669 SITTDHISPAGNIKASSPAGLYLQSLGVAPEDFNSYGSRRGNHEVMMRGTFANIRIRNEM 728

Query: 701 AIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVR 760
             + G  ++G     +P G    +++A   Y     PL++IAG +YG GSSRDWAAKG  
Sbjct: 729 --LGG--EEGGNTLYQPSGEKLSIYDAAMRYQAEGVPLVVIAGKEYGTGSSRDWAAKGTN 784

Query: 761 LAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRA 817
           L GV+A++AE FERIHR+NL+GMGVL L+F   + R + G++G E   + G    I PR 
Sbjct: 785 LLGVKAVIAESFERIHRSNLIGMGVLALQFVNDQTRQSLGLNGMEKLSIRGLDADIKPRQ 844

Query: 818 DLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
            LTV + R +G R    V  R+DT  EV  ++AGG+L
Sbjct: 845 MLTVDVERADGSRDSFQVLSRIDTLNEVQYFKAGGIL 881


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: 1952
Number of extensions: 96
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: 891
Length adjustment: 43
Effective length of query: 824
Effective length of database: 848
Effective search space:   698752
Effective search space used:   698752
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