Aligments for a candidate for acnD in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for acnD in Phaeobacter inhibens BS107

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF1856 PGA1_c18830 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Phaeo:GFF1856
          Length = 895

 Score =  688 bits (1776), Expect = 0.0
 Identities = 389/897 (43%), Positives = 536/897 (59%), Gaps = 48/897 (5%)

Query: 6   NTQYRKPLP--GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEP--EMLTAS 61
           N + R+ L   G ++ Y+    A EA   G +AKLP   +V+ EN++R  +    + T  
Sbjct: 9   NAKTRRKLSAGGKSISYYSIPAATEA-GLGDFAKLPAALKVVLENMLRFEDGGFSVSTDD 67

Query: 62  LKQIIE-----SKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVV 116
           +K   E      K   +  + PARV+  D  G  A+VDLA +RD I A GGD  ++NP+ 
Sbjct: 68  IKAFAEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIKALGGDAQKINPLN 127

Query: 117 PTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIM 176
           P  L++DHS+ ++  G  + AF  N   E  RN +R+ F+ W Q AF N  V+P G GI 
Sbjct: 128 PVDLVIDHSVMIDEFGNPR-AFQMNVDREYERNMERYQFLKWGQGAFNNFRVVPPGTGIC 186

Query: 177 HQINLERMSPVIHA---RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLG 231
           HQ+NLE ++  I +   +NG  VA+PDTLVGTDSHT  V+   V+  GVGG+EAE+ MLG
Sbjct: 187 HQVNLEYLAQTIWSDEDQNGDMVAYPDTLVGTDSHTTMVNGAAVLGWGVGGIEAEAAMLG 246

Query: 232 RASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGD 291
           +   M +P++IG ELTG    G T TD+VL + E LRA+ VV  ++EF+G+G + L L D
Sbjct: 247 QPISMLIPEVIGFELTGAMVEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGKGLDTLPLAD 306

Query: 292 RATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVY 351
           RATI+NM PE+GAT   F ID +T+ YL  TGR+ +++ LVE YAK  G W D     +Y
Sbjct: 307 RATIANMAPEYGATCGFFPIDDETIRYLRNTGRDEDRIALVEAYAKENGFWRDADYAPIY 366

Query: 352 PRTLHFDLSSVVRTIAGPSNPHARVPTSELAAR-------------GISGEVENEPGLMP 398
             TL  D+ ++V  I+GP  P   V  +   A              G    V+ E   M 
Sbjct: 367 TDTLSLDMGTIVPAISGPKRPQDYVALTGAKAAFQKEMEETFKRPMGKEIAVKGEDYTME 426

Query: 399 DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEA 458
            G V+IA+ITSCTNTSNP  +I AGL+AR A A GL RKPWVKTSLAPGS+ V  YLE A
Sbjct: 427 SGKVVIASITSCTNTSNPYVMIGAGLVARKAAALGLDRKPWVKTSLAPGSQVVSAYLEAA 486

Query: 459 NLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPY 518
           NL  +L+ +GF +VG+ CTTC G SG +   +   + + DL AT+VLSGNRNF+GRI P 
Sbjct: 487 NLQEDLDKIGFNLVGYGCTTCIGNSGPIQQELSDAIAEGDLVATSVLSGNRNFEGRISPD 546

Query: 519 AKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVK 578
            +  +LASPPLVVAYA+AGT+  D+  D +  DKDG  V L +IWPS  EI  ++ A+V 
Sbjct: 547 VRANYLASPPLVVAYALAGTMDIDLATDPIAQDKDGNDVYLKDIWPSQKEIADLVEATVT 606

Query: 579 PEQFRKVYEPMFD-----LSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERT---LK 630
            E F   Y  +F       +V+  D  +  YDW   STYI+ PPY++G      T   +K
Sbjct: 607 REAFLSKYADVFKGDEKWQAVETTD--AETYDWPAASTYIQNPPYFQGMGTEPGTISNIK 664

Query: 631 GMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRAT 690
             +PL +LGD +TTDH+SP+ +    + AG+YL    +   +FNSY + RG+H    R T
Sbjct: 665 DAKPLLILGDMVTTDHISPAGSFATTTPAGQYLLDRQVQPREFNSYGSRRGNHEIMMRGT 724

Query: 691 FANPKLKNEMAI-VDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQG 749
           FAN ++KNEM   V+G   +G      P+G  T ++EA   Y ++  PL++  G  YG G
Sbjct: 725 FANIRIKNEMLDGVEGGYTKG------PDGEQTSVYEASMAYQEQGIPLVVFGGEQYGAG 778

Query: 750 SSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV 809
           SSRDWAAKG  L GV+A++AE FERIHR+NLVGMGV+P EF  G+ R +  + G E   +
Sbjct: 779 SSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLTGDETVSI 838

Query: 810 IG--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLES 864
            G  +I P+ +++  IT  +G    + + CR+DTA E+   E GGVL    ++  +S
Sbjct: 839 HGLDTIKPQEEVSCDITYGDGTTKTITLKCRIDTAPEIEYIEHGGVLHYVLRNLAKS 895


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: 1966
Number of extensions: 100
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: 895
Length adjustment: 43
Effective length of query: 824
Effective length of database: 852
Effective search space:   702048
Effective search space used:   702048
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, or view the source code.

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