Alignments for a candidate for acnD in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Psychromonas ingrahamii 37

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_011770425.1 PING_RS10955 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000015285.1:WP_011770425.1
          Length = 891

 Score =  695 bits (1794), Expect = 0.0
 Identities = 381/854 (44%), Positives = 541/854 (63%), Gaps = 48/854 (5%)

Query: 37  KLPYTSRVLAENLVR--------RCEPEMLTASLKQIIESKQELDFPWFPARVVCHDILG 88
           +LP + +VL ENL+R        R E E L +S  Q   S  E+++   PARV+  D  G
Sbjct: 39  RLPVSIKVLLENLLRHQQDNGGSRKEIEALASS--QGRGSTTEINYQ--PARVLMQDFTG 94

Query: 89  QTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRR 148
             A+VDLA +R+A+  +G DP ++NP+    L++DHS+ V+     K AF +N AIE  R
Sbjct: 95  VPAVVDLAAMRNALVKQGLDPQKINPLAKVDLVIDHSVNVDKFS-SKSAFDENVAIEMAR 153

Query: 149 NEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN----GVAFPDTLVGTD 204
           N++R+ F+ W ++AF+N  V+P G GI HQ+NLE ++ V+ +       + +PDTLVGTD
Sbjct: 154 NKERYEFLKWGKQAFENFSVVPPGTGICHQVNLEYLAKVVWSETTENESLVYPDTLVGTD 213

Query: 205 SHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALT 264
           SHT  ++ALGV+  GVGG+EAE+VMLG+   M++PD++G ELTG+   GITATD+VL + 
Sbjct: 214 SHTTMINALGVLGWGVGGIEAEAVMLGQPISMQIPDVVGFELTGRLAEGITATDLVLQVV 273

Query: 265 EFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGR 324
           + LR   VV  ++EF+G G   L L DRATI+NM PE+GAT   F +DQQTL+YL LTGR
Sbjct: 274 QMLRKHGVVGKFVEFYGAGLAHLPLADRATIANMAPEYGATCGFFPVDQQTLNYLQLTGR 333

Query: 325 EAEQVKLVETYAKTAGLWSDDLK-QAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAA 383
           + + + LVE+Y+K  GLW D+   +A +  TL  D+S +   +AGP  P  RVP  +L  
Sbjct: 334 DKQTIDLVESYSKLQGLWRDETTPKADFSDTLLLDMSDIEPNLAGPDRPQDRVPMRQLKT 393

Query: 384 R-----GISGEVENEPGLMP---------DGAVIIAAITSCTNTSNPRNVIAAGLLARNA 429
                  ++G+ + +    P          G+++IAAITSCTNTSNP  ++AAGLLA+ A
Sbjct: 394 ATDDFIDLNGKGQQKTTDFPINDSDQSLHHGSLVIAAITSCTNTSNPAVMLAAGLLAKKA 453

Query: 430 NAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPV 489
            AKGL ++PWVKTSLAPGS+ V  YL E  L   L +LGF +VG+ CTTC G SG L   
Sbjct: 454 LAKGLVKQPWVKTSLAPGSRVVTDYLVETGLQQSLNTLGFNLVGYGCTTCIGNSGPLPKP 513

Query: 490 IQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLG 549
           +Q+ + + DL  +AVLSGNRNF GRIHP  K ++LASPPLVVAY++AGT R D+ +D +G
Sbjct: 514 VQECIEENDLIVSAVLSGNRNFAGRIHPQVKASWLASPPLVVAYSLAGTTRIDLSQDPIG 573

Query: 550 LDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFD-----LSVDYGDKVSPLY 604
              DG+ V L +IWPS+AEI  ++  SV  + F K Y  +FD      ++  G++ +  Y
Sbjct: 574 TGSDGEKVYLKDIWPSNAEITELL-KSVSHQMFEKRYSAVFDGDKEWQAIQSGEEAN--Y 630

Query: 605 DWRPQSTYIRRPPYWEGALAGE-RTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYL 663
            +  +STYI++PP++E         +     L +LGD++TTDH+SP+ AI  DS A ++L
Sbjct: 631 QFSDESTYIQKPPFFEPQYRDNFSNIVDAPILVMLGDSVTTDHISPAGAIPKDSPAAQFL 690

Query: 664 HKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTR 723
              G+ E+DFNSY + RG+H    R TF N +++NEM       K+G    ++ +     
Sbjct: 691 RNHGIDEKDFNSYGSRRGNHEIMMRGTFGNIRIRNEMT----PDKEGGYTHLQGQSQAMF 746

Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783
           +++A   Y   K+  ++IAG +YG GSSRDWAAKG  L G +A++AE FERIHR NL GM
Sbjct: 747 IFDAAMRYQQEKRSSVVIAGKEYGMGSSRDWAAKGTLLLGAKAVIAESFERIHRANLAGM 806

Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVI---GSIAPRADLTVIITRKNGERVEVPVTCRLD 840
           GVLPL+F AGE+R +  + G E FD++   G +     L  +I   +G++ ++ +  RLD
Sbjct: 807 GVLPLQFMAGEDRKSLQLTGDESFDIMGLEGEMNANQTLDAVIHYPSGKQRKIQLLSRLD 866

Query: 841 TAEEVSIYEAGGVL 854
           TA EV  Y AGGVL
Sbjct: 867 TAIEVDYYRAGGVL 880


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: 1791
Number of extensions: 89
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 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