GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Bacillus altitudinis 41KF2b

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_008343808.1 BA79_RS03665 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000691145.1:WP_008343808.1
          Length = 909

 Score = 1074 bits (2777), Expect = 0.0
 Identities = 535/898 (59%), Positives = 672/898 (74%), Gaps = 5/898 (0%)

Query: 2   KNSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRED 61
           +++FQ+ KT +T   TY YY L+ LE++G+  VS+LP+SI+V+LES+LR  DG  + +E 
Sbjct: 10  QDAFQSRKTFSTNGKTYHYYSLEALEKQGIGNVSKLPYSIKVLLESVLRQVDGRVIKKEH 69

Query: 62  IEALARW-RPDPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120
           +E LA+W   +  EI+VP K +RVILQDFTGVPAVVDLA++R A+   GGDP +INP +P
Sbjct: 70  VENLAKWGTAEVKEIDVPFKPSRVILQDFTGVPAVVDLASLRKAMADVGGDPDKINPEIP 129

Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180
            DLVIDHSVQVD  GT  A   N++ E+ERN ERY  L WA+ A  N++ VPP TGIVHQ
Sbjct: 130 VDLVIDHSVQVDKAGTEDALNINMDLEFERNAERYNFLSWAKKAFNNYQAVPPATGIVHQ 189

Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240
           VN+EYL  VV   + DG  + +PD+LVGTDSHTTM+NG+GVLGWGVGGIEAEA MLGQP 
Sbjct: 190 VNLEYLASVVHAIEEDGEIITYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLGQPS 249

Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300
           Y   P V+G KL GELP G TATDL L VT++LR+ GVV KFVEF+GPGVA+L   DRAT
Sbjct: 250 YFPVPEVIGAKLVGELPNGTTATDLALKVTQVLREKGVVNKFVEFFGPGVAQLPLADRAT 309

Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360
           IANMAPEYGAT GFFPVDEE L YLR TGR EE + +VE Y++A GLF TP+AEE + ++
Sbjct: 310 IANMAPEYGATCGFFPVDEEALAYLRLTGRDEEQINIVEEYSRANGLFYTPDAEEPI-FT 368

Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKV-LV 419
           + +E+DLS +E +L+GPKRPQD +PL ++K++F  H+  P   +GFGL + +L +++   
Sbjct: 369 DVVEIDLSQIESNLSGPKRPQDLIPLSQMKETFHKHIESPAGNQGFGLEKSELDKQIEFD 428

Query: 420 KRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGS 479
               E+  +  G++ IAAITSCTNTSNP V++GAGL+AKKA E G+    +VKTSLAPGS
Sbjct: 429 LANGEKAVMKTGAIAIAAITSCTNTSNPYVLIGAGLVAKKASELGMKVPNYVKTSLAPGS 488

Query: 480 KVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGN 539
           KVVT YL  SGL+P+L  LGF++VGYGCTTCIGNSGPL ++I  AV E +L++ +VLSGN
Sbjct: 489 KVVTGYLVNSGLLPYLRDLGFNIVGYGCTTCIGNSGPLEKEIEDAVSENDLLITSVLSGN 548

Query: 540 RNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEE 599
           RNFEGRI+P VK NYLASP LVVAYALAG ++ID T +P+G D NG+ +Y  DIWPSM+E
Sbjct: 549 RNFEGRIHPLVKGNYLASPPLVVAYALAGTVNIDLTKDPIGVDKNGENVYFNDIWPSMDE 608

Query: 600 IREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER 659
           I   ++ T+ PELF+ EY  VF+ ++RW  +      LY+WD  STYI NPPFFE+L   
Sbjct: 609 INSVVKSTVTPELFRSEYETVFDNNDRWNEIKTTDDALYKWDENSTYIDNPPFFENLSVE 668

Query: 660 --KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGN 717
             KVE ++G RV+   GDSVTTDHISPAGAI   +PAG+YL  +GV P DFNSYGSRRGN
Sbjct: 669 PGKVEPLKGLRVVAKFGDSVTTDHISPAGAIGKDTPAGKYLQERGVSPRDFNSYGSRRGN 728

Query: 718 HEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEY 777
           H VMMRGTFANIRIKN +  G EGGY    P G+V  +Y+  MRYK +GT L ++AGK+Y
Sbjct: 729 HHVMMRGTFANIRIKNQIAPGTEGGYTTYWPTGEVTSIYDACMRYKEDGTGLAILAGKDY 788

Query: 778 GTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEV 837
           G GSSRDWAAKGT LLGI+ VLAESFERIHRSNLV MGVLPL+F  GE+ ET GLTG E 
Sbjct: 789 GMGSSRDWAAKGTNLLGIKFVLAESFERIHRSNLVFMGVLPLQFKDGESAETYGLTGTET 848

Query: 838 YDILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
           +++   E ++PR LV + A   DG+E  F+ I R D+ VE+DYY++GGILQ VL   L
Sbjct: 849 FEVDVDETVRPRDLVTVKAIDTDGNEKTFEVIVRFDSEVEIDYYRHGGILQMVLREKL 906


Lambda     K      H
   0.317    0.137    0.399 

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: 2188
Number of extensions: 112
Number of successful extensions: 5
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: 902
Length of database: 909
Length adjustment: 43
Effective length of query: 859
Effective length of database: 866
Effective search space:   743894
Effective search space used:   743894
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 (21.6 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