GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Herbaspirillum seropedicae SmR1

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 HSERO_RS14940 HSERO_RS14940 aconitate hydratase

Query= SwissProt::P70920
         (906 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS14940 HSERO_RS14940 aconitate
           hydratase
          Length = 903

 Score =  957 bits (2473), Expect = 0.0
 Identities = 506/915 (55%), Positives = 643/915 (70%), Gaps = 25/915 (2%)

Query: 3   SLDSFKCKKTLKV-GAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKK 61
           S ++    K  K+ G+K   +YSLP  +K+    IS+LP S++++LE++LRN DG+ V +
Sbjct: 2   SRNTLNTLKEFKISGSKKGKFYSLPALQKSLGVNISRLPVSIRIVLESVLRNCDGQKVTE 61

Query: 62  ADIVAVSKWLRKKSLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPL 121
             +  ++ W  K +   EI F  ARV++QDFTGVP + DLAAMRN   KLG + + I PL
Sbjct: 62  EHVKQLANWGAKAARVDEIPFVVARVVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEPL 121

Query: 122 VPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGIC 181
           VPVDLV+DHSV ++ F + KA   N+  E+ +N ERY+F+KWG  AF  F VVPPG GI 
Sbjct: 122 VPVDLVVDHSVQIDHFREKKALDLNMKLEFSRNNERYQFMKWGMQAFDTFGVVPPGFGIV 181

Query: 182 HQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIE 241
           HQVNLEYL++ V  K         TG +   YPD+LVGTDSHTTM+NG+ V+GWGVGGIE
Sbjct: 182 HQVNLEYLARGVHNK---------TGVY---YPDTLVGTDSHTTMINGIGVVGWGVGGIE 229

Query: 242 AEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGL 301
           AEA MLGQP+  L P+VVG  L GA++EGVTATDLVLT+T++LR+  VVGKFVEFFG G 
Sbjct: 230 AEAGMLGQPVYFLTPDVVGVNLTGALREGVTATDLVLTITELLRQTKVVGKFVEFFGEGT 289

Query: 302 DHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRT 361
           + LS+ D+ATIANMAPEYGAT GFFPVD A I+Y K +GR    +   +AY KAQ L+  
Sbjct: 290 ESLSLTDRATIANMAPEYGATMGFFPVDDATIEYFKGTGRTKAEIDAFEAYFKAQELYGV 349

Query: 362 AKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALA-----NEYKKTEE 416
            K+    +T+ ++LDL  V PS+AGPKRP+ RI + +V   FS         N + K  E
Sbjct: 350 PKAGQIDYTQEVSLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFTKPTAENGFNKKAE 409

Query: 417 PAKRFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTS 476
                       ++ +GDV+IAAITSCTNTSNPSVL+ AGLLA+ A   GLK  P +KTS
Sbjct: 410 DLGASYKNADGVDLHNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTS 469

Query: 477 LAPGSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAA 536
           LAPGS+VV  YL  +GL  +L+K+GF +  +GCTTCIGN+G L   ++++I  N +VAAA
Sbjct: 470 LAPGSRVVTKYLEAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPAMNEAIVKNDVVAAA 529

Query: 537 VLSGNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIW 596
           VLSGNRNFE R+ P+++AN+LASPPLVVA+A+AG+VT++L  EP+G+GK GK +YL DIW
Sbjct: 530 VLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNVTRDLMTEPVGKGKGGKDIYLGDIW 589

Query: 597 PTSKEINAFMKKFVTASIFKKKYADVFKGDTN--WRKIKTV-ESETYRWNMSSTYVQNPP 653
           PTS+EI   +K  + A  FK+ YADV KG     W  IK V + E Y W  SSTY+  PP
Sbjct: 590 PTSQEIEKLLKFAMNAKTFKENYADV-KGAPGKLWEAIKGVAKGEVYNW-PSSTYIAEPP 647

Query: 654 YFEGMKKEPE-PVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADF 712
           +FE   +EP+     I  AR L +FGD ITTDHISPAGSIK +SPAGK+L  + V  ADF
Sbjct: 648 FFENFSEEPKAAAAGITGARALGVFGDSITTDHISPAGSIKESSPAGKWLQANGVLKADF 707

Query: 713 NQYGTRRGNHEVMMRGTFANIRIKNFMLKG-ADGNIPEGGLTKHWPDGEQMSIYDAAMKY 771
           N YG+RRGNHE+MMRGTFAN+RIKN M+    DG+  EGG+T H P GE+MSIYDAAMKY
Sbjct: 708 NSYGSRRGNHEIMMRGTFANVRIKNLMIPAKEDGSRVEGGITIHQPSGEEMSIYDAAMKY 767

Query: 772 QQEQVPLVVFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFE 831
             E  P +VF G EYG GSSRDWAAKGT+LLGV+AVI +SFERIHRSNLVGMGVLPL F 
Sbjct: 768 VAEGTPTMVFGGEEYGTGSSRDWAAKGTQLLGVKAVIARSFERIHRSNLVGMGVLPLQFL 827

Query: 832 EGTSWSSLGLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYY 891
              S  SLG+ GDE   L+GL G++KP+Q+ T  I   +G  + V LL RIDT  E+DYY
Sbjct: 828 GNDSVQSLGITGDETFDLKGLEGEIKPQQEATLVIHRKNGETKEVKLLLRIDTPIEVDYY 887

Query: 892 RNGGILHYVLRKLAA 906
           ++GGIL +VLR+L A
Sbjct: 888 KHGGILPFVLRQLLA 902


Lambda     K      H
   0.317    0.134    0.393 

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: 2164
Number of extensions: 102
Number of successful extensions: 6
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: 906
Length of database: 903
Length adjustment: 43
Effective length of query: 863
Effective length of database: 860
Effective search space:   742180
Effective search space used:   742180
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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