GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Burkholderia phytofirmans PsJN

Align 2-methylisocitrate dehydratase (EC 4.2.1.99) (characterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase

Query= reanno::acidovorax_3H11:Ac3H11_1140
         (980 letters)



>FitnessBrowser__BFirm:BPHYT_RS33980
          Length = 905

 Score = 1313 bits (3399), Expect = 0.0
 Identities = 682/970 (70%), Positives = 768/970 (79%), Gaps = 74/970 (7%)

Query: 14  HAFANTLKSFRTASGKDGQFYSLPALAKQFP-EIKRLPVSIRIVLESVLRNCDGRKVTPE 72
           H    TLK F + SGK G+FYSLP L K    +I RLPVSIRIVLESVLRN DG+K+  E
Sbjct: 3   HNLHKTLKEFDSGSGK-GKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAEE 61

Query: 73  HVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAKLGKNPKKIEPLV 132
           H+EQLA W P A R DEIPFVVSRVVLQDFTGVPLLAD+AAMR VA  +GK+PK IEPLV
Sbjct: 62  HIEQLANWKPTAARVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAKHMGKDPKSIEPLV 121

Query: 133 PVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDTFGVVPPGFGIVH 192
           PVDLVVDHS+ IDH+ +KN+LDLNMKLEFQRN ERY+FMKWGMQAFDTF VVPPG GIVH
Sbjct: 122 PVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIVH 181

Query: 193 QVNLEYLARGVHKRKDG---VFYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAMLGQP 249
           QVNLEYLARGVHK+ +G   V+YPD+LVGTDSHTTMINGIGVVGWGVGGIEAEA MLGQP
Sbjct: 182 QVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 241

Query: 250 VYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRA 309
           VYFLTPDVVG E+ G+LREG+TATDLVLTVTELLRK KVVGKFVEFFGEGT++L+LPDRA
Sbjct: 242 VYFLTPDVVGVELKGKLREGLTATDLVLTVTELLRKEKVVGKFVEFFGEGTKSLSLPDRA 301

Query: 310 TIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGVPLAGEVDYS 369
           TIGNMAPEYGATMGFFPVDEKTI+YF+GTGRT AEI AFE YFKAQGLFG+P AG++DY+
Sbjct: 302 TIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDAEISAFENYFKAQGLFGIPKAGQIDYT 361

Query: 370 QVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAELLHTRFHIH 429
           +VVTLDLG+VTPSLAGPKRPQDRIE+G V   F+DLFS+P A NGF + A          
Sbjct: 362 KVVTLDLGTVTPSLAGPKRPQDRIEIGHVKSTFSDLFSKPVAENGFAKKA---------- 411

Query: 430 RAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGADPTVGNGDV 489
                                               A  EA+  T  + G D  V NGD+
Sbjct: 412 ------------------------------------ADLEAQYTT--SNGVD--VKNGDI 431

Query: 490 LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLP 549
           LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGL V PHIKTSLAPGSRIVTEYL++T L+ 
Sbjct: 432 LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTDLMK 491

Query: 550 YLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEARIHPNLKAN 609
           YL+KLGF++A YGCTTCIGNAGDLTPELNEAIT+ND+V AAVLSGNRNFEARIHPN++AN
Sbjct: 492 YLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRAN 551

Query: 610 FLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALLKFAMKGKAF 669
           FLASPPLVVAYAIAG + +DLMTEPVG+GKGGKDIYLGDIWP+S+EV+ LLKFA+   AF
Sbjct: 552 FLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDIYLGDIWPTSEEVNELLKFALDADAF 611

Query: 670 RDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANKASGTRGEGQ 729
           R NY+ + T  G LW KI+G  G  Y WP STYIAEPPFF             G     Q
Sbjct: 612 RKNYSAL-TKKGDLWSKIEGEEGQVYDWPKSTYIAEPPFF-------------GKDFSMQ 657

Query: 730 KDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKADFNSYGARRG 789
               + +V  AR + +FGDS+TTDHISPAGSIKE SPAG+WL ++GVQKADFNSYG+RRG
Sbjct: 658 PADSIAAVKDARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRG 717

Query: 790 NHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFDAAMQYMAQG 849
           NHDVM+RGTFANVRIKNLMIP  ADG+R EGG+T+ Q      GE++ I+DAAM+Y+  G
Sbjct: 718 NHDVMMRGTFANVRIKNLMIPAKADGTRVEGGLTIHQP----SGEQLSIYDAAMKYIDAG 773

Query: 850 TPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFKAGDS 909
           TPTVVFAGEEYGTGSSRDWAAKGTQLLG+K VVARSFERIHRSNLVGMGVLPLQFK  DS
Sbjct: 774 TPTVVFAGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPLQFKGSDS 833

Query: 910 WETLGLTGNEVIDVLPDPA-LTPQSDARLVIRRADGTVREVVVTLRIDTPIEVDYYRAGG 968
            ++LG+TG E  D+    A   PQ +  LVIR  +G  + V V LRIDTPIEVDYY+ GG
Sbjct: 834 VQSLGITGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRVQVLLRIDTPIEVDYYKHGG 893

Query: 969 ILPFVLRQLL 978
           ILPFVLR LL
Sbjct: 894 ILPFVLRSLL 903


Lambda     K      H
   0.318    0.136    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: 2504
Number of extensions: 100
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 980
Length of database: 905
Length adjustment: 44
Effective length of query: 936
Effective length of database: 861
Effective search space:   805896
Effective search space used:   805896
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 (21.7 bits)
S2: 57 (26.6 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