Alignments for a candidate for acnD in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Klebsiella variicola At-22

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_012968443.1 KVAR_RS15100 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000025465.1:WP_012968443.1
          Length = 890

 Score =  711 bits (1836), Expect = 0.0
 Identities = 394/865 (45%), Positives = 538/865 (62%), Gaps = 42/865 (4%)

Query: 33  GAYAKLPYTSRVLAENLVRRCEPEMLT-----ASLKQIIESKQELDFPWFPARVVCHDIL 87
           G  ++LP + +VL ENL+R  + + +T     A    + ++  + +  + PARV+  D  
Sbjct: 33  GDLSRLPKSLKVLMENLLRWQDGDSVTEEDIRALAGWLQQAHADREIAYRPARVLMQDFT 92

Query: 88  GQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDR 147
           G  A+VDLA +R+A+   GGD A+VNP+ P  L++DHS+ V+  G D +AF  N  +E  
Sbjct: 93  GVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFG-DDEAFEDNVRLEME 151

Query: 148 RNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR--NG--VAFPDTLVGT 203
           RN +R+ F+ W Q+AF    V+P G GI HQ+NLE +   + +   NG  +A+PDTLVGT
Sbjct: 152 RNHERYAFLRWGQQAFSRFSVVPPGTGICHQVNLEYLGRAVWSEEVNGKWMAWPDTLVGT 211

Query: 204 DSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLAL 263
           DSHT  ++ LGV+  GVGG+EAE+ MLG+   M +PD++G +L+GK + GITATD+VL +
Sbjct: 212 DSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGFKLSGKLREGITATDLVLTV 271

Query: 264 TEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTG 323
           T+ LR   VV  ++EF+G+G + L L DRATI+NM PE+GAT   F ID  TL Y+ L+G
Sbjct: 272 TQMLRQHGVVGKFVEFYGDGLDTLPLADRATIANMAPEYGATCGFFPIDDVTLSYMRLSG 331

Query: 324 REAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELA- 382
           R  EQV LVE YAK  G+W     + V+  TL  D+ SV  ++AGP  P  RV   E+  
Sbjct: 332 RSEEQVALVEAYAKAQGMWRQPGDEPVFTSTLALDMGSVEASLAGPKRPQDRVALGEVPK 391

Query: 383 ARGISGEVE-NEPGL---------------MPDGAVIIAAITSCTNTSNPRNVIAAGLLA 426
           A   SGE+E N P                 +PDGAV IAAITSCTNTSNP  ++AAGLLA
Sbjct: 392 AFAASGELEVNHPQRQRQPVDYTLNGHHYSLPDGAVAIAAITSCTNTSNPSVLMAAGLLA 451

Query: 427 RNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGAL 486
           + A  +GL  +PWVK SLAPGSK V  YL  A L P L+ LGF +VG+ CTTC G SG L
Sbjct: 452 KKAVERGLQPQPWVKASLAPGSKVVSDYLAHAGLTPYLDQLGFNLVGYGCTTCIGNSGPL 511

Query: 487 DPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKD 546
              I++ +   DL   AVLSGNRNF+GRIHP  K  +LASPPLVVAYA+AG +  D+ ++
Sbjct: 512 PEPIEEAIKKGDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNIDLTRE 571

Query: 547 VLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGD---KVSPL 603
            LG   DG+PV L +IWPS  EI A     V  E FRK Y  +F  + ++     + S  
Sbjct: 572 PLGQGSDGEPVYLKDIWPSGEEI-ARAVEQVSTEMFRKEYAEVFSGTEEWKAIKVEASDT 630

Query: 604 YDWRPQSTYIRRPPYWEGALAGE----RTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659
           YDW+  STYIR  P+++  +  E      + G R LA+LGD++TTDH+SP+ +I  DS A
Sbjct: 631 YDWQEDSTYIRLSPFFD-EMGVEPLPVEDIHGARILAMLGDSVTTDHISPAGSIKADSPA 689

Query: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEG 719
           G YL + G+   DFNSY + RG+H    R TFAN +++NEM  V G   +G + R  P+ 
Sbjct: 690 GRYLQEHGVARRDFNSYGSRRGNHEVMMRGTFANIRIRNEM--VPG--VEGGMTRHLPDR 745

Query: 720 IVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
               +++A   Y     PL +IAG +YG GSSRDWAAKG RL G+  ++AE FERIHR+N
Sbjct: 746 EPVAIYDAAMQYKAEGIPLAVIAGKEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSN 805

Query: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDV--IGSIAPRADLTVIITRKNGERVEVPVTC 837
           L+GMG+LPLEF  G  R T  + G E  D+  + S+ P A + V +TR +G +  +P  C
Sbjct: 806 LIGMGILPLEFPQGVTRKTLQLTGEERIDISNLQSLQPGATVPVTLTRPDGSQEVIPCRC 865

Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFL 862
           R+DTA E++ Y   G+L    ++ L
Sbjct: 866 RIDTATELTYYRNDGILHYVIRNML 890


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: 1965
Number of extensions: 102
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: 890
Length adjustment: 43
Effective length of query: 824
Effective length of database: 847
Effective search space:   697928
Effective search space used:   697928
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