GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Lysobacter daejeonensis GH1-9

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_036133359.1 N800_RS00150 aconitate hydratase AcnA

Query= SwissProt::Q8NQ98
         (939 letters)



>NCBI__GCF_000768355.1:WP_036133359.1
          Length = 926

 Score = 1044 bits (2700), Expect = 0.0
 Identities = 539/947 (56%), Positives = 671/947 (70%), Gaps = 43/947 (4%)

Query: 6   NSFNAKSTLEVGDKSYDYFALSAVP---GMEKLPYSLKVLGENLLRTEDGA-NITNEHIE 61
           +SF+ +  L V  KS  Y++L A+     + KLPYS+K+L ENLLR EDG   +  EHIE
Sbjct: 3   DSFSTRRQLSVNGKSLTYYSLPALGEHFDLSKLPYSMKILLENLLRHEDGGMTVGREHIE 62

Query: 62  AIANWDASSDPSIEIQFTPARVLMQDFTGVPCVVDLATMREAVAALGGDPNDVNPLNPAE 121
           A+A WDA+ DP  EI F PARV++QDFTGVPCVVDLA MR+AV  LGG+   +NPL P+E
Sbjct: 63  AVAQWDATKDPDTEIAFMPARVVLQDFTGVPCVVDLAAMRDAVTRLGGNARQINPLIPSE 122

Query: 122 MVIDHSVIVEAFGRPDALAKNVEIEYERNEERYQFLRWGSESFSNFRVVPPGTGIVHQVN 181
           +VIDHSV V+ FGRPDAL  N +IE+ERN ERY FLRWG ++F NF+VVPP TGIVHQVN
Sbjct: 123 LVIDHSVQVDVFGRPDALDLNGKIEFERNMERYSFLRWGQKAFENFKVVPPNTGIVHQVN 182

Query: 182 IEYLARVVFDNEGL---------AYPDTCIGTDSHTTMENGLGILGWGVGGIEAEAAMLG 232
           +E LARVV + E           A+PDT  GTDSHTTM NG+G+LGWGVGGIEAEAAMLG
Sbjct: 183 LENLARVVVEREVKTDDGASELQAFPDTVFGTDSHTTMINGIGVLGWGVGGIEAEAAMLG 242

Query: 233 QPVSMLIPRVVGFKLTGEIPVGVTATDVVLTITEMLRDHGVVQKFVEFYGSGVKAVPLAN 292
           QP SMLIP+VVGFKLTG++P G TATD+VLT+T+MLR  GVV KFVEFYG G++ +PLA+
Sbjct: 243 QPSSMLIPQVVGFKLTGKLPEGTTATDLVLTVTQMLRKLGVVGKFVEFYGEGLQHLPLAD 302

Query: 293 RATIGNMSPEFGSTCAMFPIDEETTKYLRLTGRPEEQVALVEAYAKAQGMWLDEDTVEAE 352
           RATI NM+PE+G+TC +FPID E   YLRL+GR E Q+ALVEAYAKAQG+W +    EA 
Sbjct: 303 RATIANMAPEYGATCGIFPIDAEALNYLRLSGRSEAQIALVEAYAKAQGLWHEPGAPEAT 362

Query: 353 YSEYLELDLSTVVPSIAGPKRPQDRILLSEAKEQFRKDLPTYTDDAVSVDTSIPATRMVN 412
           YS  L LDL  V PS+AGPKRPQDR+LL + +  F  +L T              +    
Sbjct: 363 YSATLSLDLGDVKPSLAGPKRPQDRVLLEDMQVNFNDNL-TGLIVGRKARVGCAESDFKE 421

Query: 413 EGGGQPEGGVEADNYNASWAGSGESLATGAEGRPSKPVTVASPQGGEYTIDHGMVAIASI 472
           EGG QP+                      A    +KP +       +  +  G V IA+I
Sbjct: 422 EGGAQPQ----------------------ASHLAAKPQSKIRIHDQDAYLHDGSVVIAAI 459

Query: 473 TSCTNTSNPSVMIGAGLIARKAAEKGLKSKPWVKTICAPGSQVVDGYYQRADLWKDLEAM 532
           TSCTNTSNP+VM+GAGL+AR AA+ GLK+KPWVKT   PGS VV  Y ++A L  DLE +
Sbjct: 460 TSCTNTSNPAVMLGAGLLARNAAKLGLKAKPWVKTSLGPGSLVVTDYLRKAGLLDDLEQL 519

Query: 533 GFYLSGFGCTTCIGNSGPLPEEISAAINEHDLTATAVLSGNRNFEGRISPDVKMNYLASP 592
           GFY+ G+GCTTCIGNSGPLP+ +S  I E+DL   +VLSGNRNFEGR+ P+VKMNYLASP
Sbjct: 520 GFYVVGYGCTTCIGNSGPLPDVVSKGIAENDLVVASVLSGNRNFEGRVHPEVKMNYLASP 579

Query: 593 IMVIAYAIAGTMDFDFENEALGQDQDGNDVFLKDIWPSTEEIEDTIQQAISRELYEADYA 652
            +V+AYAIAGT+D D   + L    DG  V+L+D+WPS +EI D I   +  EL+  +YA
Sbjct: 580 PLVVAYAIAGTVDIDLTRDPLATTADGTPVYLRDLWPSNKEIGDLIAATVGPELFAQNYA 639

Query: 653 DVFKGDKQWQELDVPTGDTFEWDENSTYIRKAPYFDGMPVEPVAVTDIQGARVLAKLGDS 712
           DVFKGD +W ++  P G++F WDE STYI+  PYFDGM +    + DI+GARV+   GDS
Sbjct: 640 DVFKGDNRWNQIASPEGESFRWDEASTYIKNPPYFDGMTMAVGHIADIEGARVMGLFGDS 699

Query: 713 VTTDHISPASSIKPGTPAAQYLDEHGVERHDYNSLGSRRGNHEVMMRGTFANIRLQN-QL 771
           +TTDHISPA +IK  +PA ++L   GV+  D+NS GSRRGN +VM+RGTFANIR++N  L
Sbjct: 700 ITTDHISPAGNIKKDSPAGRFLQARGVQPADFNSYGSRRGNDDVMVRGTFANIRIKNLML 759

Query: 772 VDIAGGYTRDFTQEGA--PQAFIYDASVNYKAAGIPLVVLGGKEYGTGSSRDWAAKGTNL 829
               GG T  ++  GA   +  IYDA++ YKA G+PLVV  GKEYGTGSSRDWAAKGTNL
Sbjct: 760 GGEEGGNTLYYSPGGAAPEKLAIYDAAMKYKADGVPLVVFAGKEYGTGSSRDWAAKGTNL 819

Query: 830 LGIRAVITESFERIHRSNLIGMGVVPLQFPAGESHESLGLDGTETFDITGLTALNEGETP 889
           LG+RAV+ ESFERIHRSNL+GMGV+PLQF AGE+ ++LGLDG+ET  ITGL    +G + 
Sbjct: 820 LGVRAVVAESFERIHRSNLVGMGVLPLQFQAGENAQTLGLDGSETISITGLV---DGAS- 875

Query: 890 KTVKVTATKENGDVVEFDAVVRIDTPGEADYYRHGGILQYVLRQMAA 936
           +T  V A + +G    F+  V + TP E +Y+RHGGIL YVLRQ+AA
Sbjct: 876 RTATVVARRADGSEKRFEVKVLLLTPKEVEYFRHGGILHYVLRQLAA 922


Lambda     K      H
   0.314    0.133    0.390 

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: 2304
Number of extensions: 127
Number of successful extensions: 7
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: 939
Length of database: 926
Length adjustment: 43
Effective length of query: 896
Effective length of database: 883
Effective search space:   791168
Effective search space used:   791168
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: 42 (22.0 bits)
S2: 57 (26.6 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