GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Bacillus altitudinis 41KF2b

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_008343808.1 BA79_RS03665 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000691145.1:WP_008343808.1
          Length = 909

 Score =  715 bits (1845), Expect = 0.0
 Identities = 390/892 (43%), Positives = 558/892 (62%), Gaps = 55/892 (6%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIESK--------QE 71
           ++ + EA+E    G  +KLPY+ +VL E+++R+ +  ++    K+ +E+         +E
Sbjct: 27  HYYSLEALEKQGIGNVSKLPYSIKVLLESVLRQVDGRVIK---KEHVENLAKWGTAEVKE 83

Query: 72  LDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYG 131
           +D P+ P+RV+  D  G  A+VDLA LR A+A  GGDP ++NP +P  L++DHS+ V+  
Sbjct: 84  IDVPFKPSRVILQDFTGVPAVVDLASLRKAMADVGGDPDKINPEIPVDLVIDHSVQVDKA 143

Query: 132 GFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHA- 190
           G + DA   N  +E  RN +R++F++W +KAF N   +P   GI+HQ+NLE ++ V+HA 
Sbjct: 144 GTE-DALNINMDLEFERNAERYNFLSWAKKAFNNYQAVPPATGIVHQVNLEYLASVVHAI 202

Query: 191 -RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELT 247
             +G  + +PDTLVGTDSHT  ++ +GV+  GVGG+EAE+ MLG+ SY  +P++IG +L 
Sbjct: 203 EEDGEIITYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLGQPSYFPVPEVIGAKLV 262

Query: 248 GKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAA 307
           G+   G TATD+ L +T+ LR + VV+ ++EFFG G   L L DRATI+NM PE+GAT  
Sbjct: 263 GELPNGTTATDLALKVTQVLREKGVVNKFVEFFGPGVAQLPLADRATIANMAPEYGATCG 322

Query: 308 MFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGL-WSDDLKQAVYPRTLHFDLSSVVRTI 366
            F +D++ L YL LTGR+ EQ+ +VE Y++  GL ++ D ++ ++   +  DLS +   +
Sbjct: 323 FFPVDEEALAYLRLTGRDEEQINIVEEYSRANGLFYTPDAEEPIFTDVVEIDLSQIESNL 382

Query: 367 AGPSNPHARVPTSELAA-----------------------RGISGEVEN-EPGLMPDGAV 402
           +GP  P   +P S++                         + I  ++ N E  +M  GA+
Sbjct: 383 SGPKRPQDLIPLSQMKETFHKHIESPAGNQGFGLEKSELDKQIEFDLANGEKAVMKTGAI 442

Query: 403 IIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLP 462
            IAAITSCTNTSNP  +I AGL+A+ A+  G+    +VKTSLAPGSK V  YL  + LLP
Sbjct: 443 AIAAITSCTNTSNPYVLIGAGLVAKKASELGMKVPNYVKTSLAPGSKVVTGYLVNSGLLP 502

Query: 463 ELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQA 522
            L  LGF IVG+ CTTC G SG L+  I+  V + DL  T+VLSGNRNF+GRIHP  K  
Sbjct: 503 YLRDLGFNIVGYGCTTCIGNSGPLEKEIEDAVSENDLLITSVLSGNRNFEGRIHPLVKGN 562

Query: 523 FLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQF 582
           +LASPPLVVAYA+AGT+  D+ KD +G+DK+G+ V   +IWPS  EI++V+ ++V PE F
Sbjct: 563 YLASPPLVVAYALAGTVNIDLTKDPIGVDKNGENVYFNDIWPSMDEINSVVKSTVTPELF 622

Query: 583 RKVYEPMFDLSVDYGD---KVSPLYDWRPQSTYIRRPPYWEGALAGE----RTLKGMRPL 635
           R  YE +FD +  + +       LY W   STYI  PP++E  L+ E      LKG+R +
Sbjct: 623 RSEYETVFDNNDRWNEIKTTDDALYKWDENSTYIDNPPFFEN-LSVEPGKVEPLKGLRVV 681

Query: 636 AVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPK 695
           A  GD++TTDH+SP+ AI  D+ AG+YL + G+   DFNSY + RG+H    R TFAN +
Sbjct: 682 AKFGDSVTTDHISPAGAIGKDTPAGKYLQERGVSPRDFNSYGSRRGNHHVMMRGTFANIR 741

Query: 696 LKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWA 755
           +KN++A       +G      P G VT +++A   Y +    L I+AG DYG GSSRDWA
Sbjct: 742 IKNQIA----PGTEGGYTTYWPTGEVTSIYDACMRYKEDGTGLAILAGKDYGMGSSRDWA 797

Query: 756 AKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVF--DVIGSI 813
           AKG  L G++ ++AE FERIHR+NLV MGVLPL+FK GE+  TYG+ GTE F  DV  ++
Sbjct: 798 AKGTNLLGIKFVLAESFERIHRSNLVFMGVLPLQFKDGESAETYGLTGTETFEVDVDETV 857

Query: 814 APRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865
            PR  +TV     +G      V  R D+  E+  Y  GG+LQ   ++ L SN
Sbjct: 858 RPRDLVTVKAIDTDGNEKTFEVIVRFDSEVEIDYYRHGGILQMVLREKLASN 909


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: 1899
Number of extensions: 101
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: 909
Length adjustment: 43
Effective length of query: 824
Effective length of database: 866
Effective search space:   713584
Effective search space used:   713584
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