GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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