GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Azospirillum thiophilum BV-S

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_045580974.1 AL072_RS06770 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001305595.1:WP_045580974.1
          Length = 896

 Score =  723 bits (1867), Expect = 0.0
 Identities = 393/874 (44%), Positives = 548/874 (62%), Gaps = 40/874 (4%)

Query: 15  GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVR-----RCEPEMLTASLKQIIESK 69
           G + DYF  + A +A   G  ++LP++ +VL ENL+R         + + A  + +++ +
Sbjct: 20  GKSYDYFSLKAAEQA-GLGDLSRLPFSMKVLLENLLRFEDGRTVSVDDVKAVAQWLVDKR 78

Query: 70  QELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVE 129
            + +  + PARV+  D  G  A+ DLA +R+A+AA GGDPA++NP+VP  L++DHS+ V+
Sbjct: 79  SDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPAKINPLVPVDLVIDHSVMVD 138

Query: 130 YGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIH 189
           Y G   D+F +N  +E  RN +R+ F+ W QKAF N  V+P G GI HQ+N E +S V+ 
Sbjct: 139 YFG-GADSFQRNVDLEFERNLERYEFLRWGQKAFDNFRVVPPGTGICHQVNTEYLSQVVW 197

Query: 190 -----ARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
                +   VA+PDTLVGTDSHT  V+ L V+  GVGG+EAE+ MLG+   M +P++IG 
Sbjct: 198 TDADPSGRPVAYPDTLVGTDSHTTMVNGLSVLGWGVGGIEAEAAMLGQPISMLIPEVIGF 257

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           +LTG+ + G+TATD+VL +T+ LR + VV  ++EFFG G +++TL DRATI NM PE+GA
Sbjct: 258 KLTGRMKEGMTATDLVLTVTQMLRRKGVVGKFVEFFGPGLDSMTLPDRATIGNMAPEYGA 317

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-DLKQAVYPRTLHFDLSSVV 363
           T  +F ID +T+ YLT TGR+  +V LVE YAK  G+W + D    V+   L  D+ +V 
Sbjct: 318 TCGIFPIDAETIRYLTFTGRDPGRVALVEAYAKAQGMWREPDSPDPVFSDVLELDMGTVE 377

Query: 364 RTIAGPSNPHARVPTSELA---ARGISGE-----------VENEPGLMPDGAVIIAAITS 409
            ++AGP  P  RV  S LA   AR ++             V++    +  GAV+IAAITS
Sbjct: 378 PSLAGPKRPQDRVALSALAQGFARDMAEAYKADDPKKAVPVKDAGYSLEQGAVVIAAITS 437

Query: 410 CTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGF 469
           CTNTSNP  ++AAGLLA+ A  KGL +KPWVKTSLAPGS+ V  YL +A L P L+ LGF
Sbjct: 438 CTNTSNPAVLVAAGLLAKKAVEKGLAQKPWVKTSLAPGSQVVTDYLAKAGLQPYLDRLGF 497

Query: 470 GIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 529
            IVG+ CTTC G SG L   I   V D +L   AVLSGNRNF+GR++P+ +  +LASPPL
Sbjct: 498 NIVGYGCTTCIGNSGPLPEPIAAAVEDGNLVVGAVLSGNRNFEGRVNPHTRANYLASPPL 557

Query: 530 VVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPM 589
            VAYA+AG +  D+  + LG   DG+PV L +IWP++ E+   I AS+  + FR  Y  +
Sbjct: 558 CVAYALAGNLNIDLTTEPLGTGTDGQPVYLKDIWPTNREVQDAIDASLTADMFRSRYSDV 617

Query: 590 FDLSVDY---GDKVSPLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNIT 643
           F     +          Y W+  STY++ PP++ G    L     ++G R LAVLGD+IT
Sbjct: 618 FKGPEQWQAIATAEGQTYQWQDASTYVKLPPFFSGLTRTLDPVSDVRGARALAVLGDSIT 677

Query: 644 TDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIV 703
           TDH+SP+ +I   S AGEYL    +  +DFNSY   RG+H    R TFAN +++NE+   
Sbjct: 678 TDHISPAGSIKRTSPAGEYLLSHQVRLQDFNSYGARRGNHEVMMRGTFANIRIRNELL-- 735

Query: 704 DGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAG 763
                +G   +  P G    ++ A   Y D   PL+++AG +YG GSSRDWAAKG RL G
Sbjct: 736 --PGVEGGETKHYPSGERLPIYTAAMRYADEGVPLVVVAGKEYGTGSSRDWAAKGTRLLG 793

Query: 764 VEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLT 820
           ++A++AE FERIHR+NLVGMG+LPL+FK G  RA   +DG+E FD+ G    + PR D+ 
Sbjct: 794 IKAVIAESFERIHRSNLVGMGILPLQFKDGLTRADLKLDGSETFDIAGIEQDLRPRKDVA 853

Query: 821 VIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           + +TR +G      +  R+DT +EV  Y  GGVL
Sbjct: 854 LTLTRADGTVEHHTLLLRIDTLDEVEYYRNGGVL 887


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: 1981
Number of extensions: 94
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: 896
Length adjustment: 43
Effective length of query: 824
Effective length of database: 853
Effective search space:   702872
Effective search space used:   702872
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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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