Aligments for a candidate for acn in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS33980 BPHYT_RS33980 aconitate
           hydratase
          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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources