Alignments for a candidate for acnD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Herbaspirillum seropedicae SmR1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate HSERO_RS14940 HSERO_RS14940 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__HerbieS:HSERO_RS14940
          Length = 903

 Score =  668 bits (1724), Expect = 0.0
 Identities = 368/890 (41%), Positives = 533/890 (59%), Gaps = 42/890 (4%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LK 63
           +NT     + G+    F +  A++       ++LP + R++ E+++R C+ + +T   +K
Sbjct: 6   LNTLKEFKISGSKKGKFYSLPALQKSLGVNISRLPVSIRIVLESVLRNCDGQKVTEEHVK 65

Query: 64  QII----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
           Q+     ++ +  + P+  ARVV  D  G   L DLA +R+  +  G +P  + P+VP  
Sbjct: 66  QLANWGAKAARVDEIPFVVARVVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEPLVPVD 125

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           L+VDHS+ +++   +K A   N  +E  RN +R+ F+ W  +AF    V+P G GI+HQ+
Sbjct: 126 LVVDHSVQIDHFR-EKKALDLNMKLEFSRNNERYQFMKWGMQAFDTFGVVPPGFGIVHQV 184

Query: 180 NLERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLP 239
           NLE ++  +H + GV +PDTLVGTDSHT  ++ +GV+  GVGG+EAE+ MLG+  Y   P
Sbjct: 185 NLEYLARGVHNKTGVYYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTP 244

Query: 240 DIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMT 299
           D++GV LTG  + G+TATD+VL +TE LR  KVV  ++EFFGEG E+L+L DRATI+NM 
Sbjct: 245 DVVGVNLTGALREGVTATDLVLTITELLRQTKVVGKFVEFFGEGTESLSLTDRATIANMA 304

Query: 300 PEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWS-DDLKQAVYPRTLHFD 358
           PE+GAT   F +D  T++Y   TGR   ++   E Y K   L+      Q  Y + +  D
Sbjct: 305 PEYGATMGFFPVDDATIEYFKGTGRTKAEIDAFEAYFKAQELYGVPKAGQIDYTQEVSLD 364

Query: 359 LSSVVRTIAGPSNPHARV---------------PTSE----LAARGISGEVENEPGL-MP 398
           L +V  ++AGP  P  R+               PT+E      A  +    +N  G+ + 
Sbjct: 365 LGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFTKPTAENGFNKKAEDLGASYKNADGVDLH 424

Query: 399 DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEA 458
           +G V+IAAITSCTNTSNP  ++AAGLLA+ A   GL   P +KTSLAPGS+ V  YLE A
Sbjct: 425 NGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSRVVTKYLEAA 484

Query: 459 NLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPY 518
            LLP LE LGFG+  + CTTC G +G L P + + ++  D+ A AVLSGNRNF+ RIHP 
Sbjct: 485 GLLPYLEKLGFGVTAYGCTTCIGNAGDLTPAMNEAIVKNDVVAAAVLSGNRNFEARIHPN 544

Query: 519 AKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVK 578
            +  FLASPPLVVAYAIAG +  D+  + +G  K GK + L +IWP+  EI+ ++  ++ 
Sbjct: 545 IRANFLASPPLVVAYAIAGNVTRDLMTEPVGKGKGGKDIYLGDIWPTSQEIEKLLKFAMN 604

Query: 579 PEQFRKVYEPMFDLSVDYGDKV-----SPLYDWRPQSTYIRRPPYWEG----ALAGERTL 629
            + F++ Y  +        + +       +Y+W P STYI  PP++E       A    +
Sbjct: 605 AKTFKENYADVKGAPGKLWEAIKGVAKGEVYNW-PSSTYIAEPPFFENFSEEPKAAAAGI 663

Query: 630 KGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRA 689
            G R L V GD+ITTDH+SP+ +I   S AG++L   G+ + DFNSY + RG+H    R 
Sbjct: 664 TGARALGVFGDSITTDHISPAGSIKESSPAGKWLQANGVLKADFNSYGSRRGNHEIMMRG 723

Query: 690 TFANPKLKNEM--AIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYG 747
           TFAN ++KN M  A  DG   +G +   +P G    +++A   Y+    P ++  G +YG
Sbjct: 724 TFANVRIKNLMIPAKEDGSRVEGGITIHQPSGEEMSIYDAAMKYVAEGTPTMVFGGEEYG 783

Query: 748 QGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVF 807
            GSSRDWAAKG +L GV+A++A  FERIHR+NLVGMGVLPL+F   ++  + GI G E F
Sbjct: 784 TGSSRDWAAKGTQLLGVKAVIARSFERIHRSNLVGMGVLPLQFLGNDSVQSLGITGDETF 843

Query: 808 D---VIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           D   + G I P+ + T++I RKNGE  EV +  R+DT  EV  Y+ GG+L
Sbjct: 844 DLKGLEGEIKPQQEATLVIHRKNGETKEVKLLLRIDTPIEVDYYKHGGIL 893


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: 1940
Number of extensions: 98
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: 903
Length adjustment: 43
Effective length of query: 824
Effective length of database: 860
Effective search space:   708640
Effective search space used:   708640
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