GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS14940
          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:

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