GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Caulobacter crescentus NA1000

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 CCNA_03781 CCNA_03781 aconitate hydratase

Query= SwissProt::P70920
         (906 letters)



>FitnessBrowser__Caulo:CCNA_03781
          Length = 895

 Score = 1209 bits (3128), Expect = 0.0
 Identities = 614/907 (67%), Positives = 718/907 (79%), Gaps = 17/907 (1%)

Query: 1   MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60
           M S+DS K ++ LKVG ++YVYYSL  AE+ GL  +S LP SMKVLLENLLRNEDG SV 
Sbjct: 1   MASVDSLKARRELKVGKQSYVYYSLRAAEEAGLADVSSLPVSMKVLLENLLRNEDGVSVN 60

Query: 61  KADIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKIN 119
           + D+ AV+ WL  K S+EHEI+FRPARVLMQDFTGVPAVVDLAAMR+AM  LG D  KIN
Sbjct: 61  EDDLKAVAAWLNNKGSVEHEISFRPARVLMQDFTGVPAVVDLAAMRDAMVALGADPAKIN 120

Query: 120 PLVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTG 179
           PL PVDLVIDHSV+V+ FG+ KA+  NV  EY++N ERY FL+WG +AF+NF VVPPGTG
Sbjct: 121 PLNPVDLVIDHSVMVDNFGNPKAYDDNVKREYERNIERYRFLRWGSSAFNNFRVVPPGTG 180

Query: 180 ICHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGG 239
           ICHQVNLEYL+QTVWT              EVAYPD++VGTDSHTTMVNGLAVLGWGVGG
Sbjct: 181 ICHQVNLEYLAQTVWTNT--------VDGAEVAYPDTVVGTDSHTTMVNGLAVLGWGVGG 232

Query: 240 IEAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGP 299
           IEAEA MLGQP+ ML+P V+GFKL GAM EG TATDLVLTVTQMLRK GVVGKFVEF+G 
Sbjct: 233 IEAEAAMLGQPIPMLIPEVIGFKLTGAMPEGATATDLVLTVTQMLRKKGVVGKFVEFYGD 292

Query: 300 GLDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLF 359
            L +L++ D+ATIANMAPEYGATCGFFP+ AA I YLK +GRAA RVALV+AYAK QGL+
Sbjct: 293 ALANLTLEDQATIANMAPEYGATCGFFPISAATIAYLKGTGRAAERVALVEAYAKEQGLW 352

Query: 360 RTAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAK 419
                A+P FT+TL LDL+ V+PS+AGPKRP+ R+ L   A  F+ +LA E+ K E P  
Sbjct: 353 WEPGVAEPTFTDTLELDLSTVLPSLAGPKRPQDRVLLSDAAAKFAESLAGEFGKAENPEL 412

Query: 420 RFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAP 479
           R  VEG+ +++GHGDVVIAAITSCTNTSNPSVLI AGLLA+NA AKGLKAKPWVKTSLAP
Sbjct: 413 RAPVEGEDFDVGHGDVVIAAITSCTNTSNPSVLIAAGLLAKNAVAKGLKAKPWVKTSLAP 472

Query: 480 GSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLS 539
           GSQVV  YLA +GL  HLD +GFNLVG+GCTTCIGNSGPLPE ISK+INDN +VA +VLS
Sbjct: 473 GSQVVTDYLAKAGLTKHLDALGFNLVGYGCTTCIGNSGPLPEAISKTINDNDLVACSVLS 532

Query: 540 GNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTS 599
           GNRNFEGRV+PDV+ANYLASPPLVVA+ALAGS+  +LA +P+G+ K G  V+LKDIWP++
Sbjct: 533 GNRNFEGRVNPDVRANYLASPPLVVAYALAGSLKIDLATQPIGQDKKGNDVFLKDIWPSN 592

Query: 600 KEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMK 659
           ++I A  +K +   +F  +Y DVFKGD NW+ IK    +TY W   STYVQNPPYF  M 
Sbjct: 593 EDIAALQRKAINEKMFATRYGDVFKGDKNWQGIKVTGGQTYAWEADSTYVQNPPYFPNMS 652

Query: 660 KEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRR 719
             P PVTDIVEARILA+FGD ITTDHISPAGSIK +SPAGK+L ++ V P DFN YG RR
Sbjct: 653 MTPAPVTDIVEARILAVFGDSITTDHISPAGSIKASSPAGKFLIDNGVEPVDFNGYGARR 712

Query: 720 GNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLV 779
           GNH+VMMRGTFANIRI+N +         EGG+TKH+P GE MSIYDAAMKYQ+E  P V
Sbjct: 713 GNHQVMMRGTFANIRIRNRITPDI-----EGGVTKHFPTGEVMSIYDAAMKYQEEGRPAV 767

Query: 780 VFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSL 839
           VF G EYG GSSRDWAAKGT+LLGVRAVIC+SFERIHRSNLVGMGVLPL F +   W  L
Sbjct: 768 VFGGKEYGTGSSRDWAAKGTKLLGVRAVICESFERIHRSNLVGMGVLPLQFVQ-DGWQKL 826

Query: 840 GLKGDEKVTLRGLVGDLKPRQKLTAEIV-SGDGSLQRVSLLCRIDTLDELDYYRNGGILH 898
            L G+E V++RGL  DL PR++L  E+    DG + R  + CRIDT  EL+Y++NGG+L+
Sbjct: 827 ELTGEEIVSIRGLT-DLAPRKQLIVELYRPTDGRIARFPVRCRIDTPTELEYFKNGGVLN 885

Query: 899 YVLRKLA 905
           YVLR LA
Sbjct: 886 YVLRNLA 892


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: 2183
Number of extensions: 84
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: 906
Length of database: 895
Length adjustment: 43
Effective length of query: 863
Effective length of database: 852
Effective search space:   735276
Effective search space used:   735276
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