GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Magnetospirillum magneticum AMB-1

Align 2-methylisocitrate dehydratase (EC 4.2.1.99) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA

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



>lcl|NCBI__GCF_000009985.1:WP_011386009.1 AMB_RS18485 aconitate
           hydratase AcnA
          Length = 903

 Score = 1120 bits (2898), Expect = 0.0
 Identities = 585/949 (61%), Positives = 689/949 (72%), Gaps = 71/949 (7%)

Query: 32  QFYSLPAL-AKQFPEIKRLPVSIRIVLESVLRNCDGRKVTPEHVEQLARWAPNAERKDEI 90
           ++Y+L AL A     + RLPVSIRIVLESVLRNCDG+++T EHV QLA W P+A R  EI
Sbjct: 21  RYYALAALDAVTDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLANWRPDAPRTQEI 80

Query: 91  PFVVSRVVLQDFTGVPLLADLAAMRSVAAKLGKNPKKIEPLVPVDLVVDHSIMIDHYGKK 150
           PFVV+R+VLQDFTGVPLL DLAAMR VA   GKNPK IEPLVPVDLVVDHS+ +DHYG+ 
Sbjct: 81  PFVVARIVLQDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVVDHSVQVDHYGEA 140

Query: 151 NSLDLNMKLEFQRNRERYEFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHKRKDGV 210
           +SLDLNM+ EFQRN ERY F+KWGMQAFDTF VVPPG GIVHQVNLE+LARGV + KDG+
Sbjct: 141 DSLDLNMRREFQRNAERYRFIKWGMQAFDTFRVVPPGIGIVHQVNLEFLARGVLE-KDGI 199

Query: 211 FYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGFEMTGRLREGV 270
            YPDTLVGTDSHTTMIN +GV GWGVGGIEAEA MLGQP+ FLTPDVVG  + GRL EG 
Sbjct: 200 TYPDTLVGTDSHTTMINALGVAGWGVGGIEAEAGMLGQPLVFLTPDVVGVHLHGRLPEGA 259

Query: 271 TATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRATIGNMAPEYGATMGFFPVDEK 330
           TATDLVL +TE LR+ KVVGKFVEFFGEGTR+LA+PDRATI NMAPEYGATMGFFPVD++
Sbjct: 260 TATDLVLFLTERLRRAKVVGKFVEFFGEGTRSLAVPDRATIANMAPEYGATMGFFPVDKE 319

Query: 331 TIDYFQGTGRTKAEIEAFEAYFKAQGLFGVPLAGEVDYSQVVTLDLGSVTPSLAGPKRPQ 390
           T+ Y + TGRT +EIE F AY+ AQGLFG+P+ G++DYS+V+  DLGSV PS+AGPKRPQ
Sbjct: 320 TVRYLEATGRTDSEIEVFRAYYSAQGLFGMPMPGDIDYSEVIEFDLGSVQPSIAGPKRPQ 379

Query: 391 DRIELGQVSRQFADLFSQPAAHNGFNRPAELLHTRFHIHRAAEVVADVTPDGKPTPAGAP 450
           DR+ L  + R F  LFS PA  +G+ RPAE L  R  +   A   AD             
Sbjct: 380 DRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALGRRHRVETTA--AAD------------- 424

Query: 451 RSVVEMEANKPALATAHAEARSATLPARGADPTVGNGDVLIAAITSCTNTSNPSVLLAAG 510
                                            +G+GDVLIAAITSCTNTSNP V+LAAG
Sbjct: 425 ---------------------------------IGHGDVLIAAITSCTNTSNPGVMLAAG 451

Query: 511 LLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLPYLEKLGFSIAGYGCTTCIGNA 570
           LLA+KAV  GLKV P +KTSLAPGSR+VTEYL++ GLL  LE LGF +  YGCTTCIGN+
Sbjct: 452 LLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKAGLLGDLESLGFGVVAYGCTTCIGNS 511

Query: 571 GDLTPELNEAITQNDLVCAAVLSGNRNFEARIHPNLKANFLASPPLVVAYAIAGTVLKDL 630
           G L P+L +AI  +DLVCAAVLSGNRNFEARIHP +KANFL SPPLVVA+AIAG +  D+
Sbjct: 512 GPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPAIKANFLMSPPLVVAFAIAGRIAIDM 571

Query: 631 MTEPVGQGKGGKDIYLGDIWPSSDEVHALLKFAMKGKAFRDNYAKVATDPGKLWEKIQGV 690
             EP+G GK GK + L DIWPS  EV   L  A   + +R  Y+        LW  I   
Sbjct: 572 TQEPLGTGKDGKPVMLKDIWPSGREVADALLVATDPELYRRLYSDF-VHGNPLWNDIPTQ 630

Query: 691 SGTAYTWPASTYIAEPPFFAQFALEKGANKASGTRGEGQKDAQLPSVMGARIMALFGDSI 750
           +G AY W  STYIAEPPFF +F+                + A +  ++GAR +A+FGDS+
Sbjct: 631 TGPAYAWETSTYIAEPPFFERFS---------------PQPAGVGDIIGARALAIFGDSV 675

Query: 751 TTDHISPAGSIKESSPAGQWLLQHGVQKADFNSYGARRGNHDVMVRGTFANVRIKNLMIP 810
           TTDHISPAGSI  SSPAGQ+LL HGV   DFNSYGARRGNH+VM+RGTFANVRI+NLM+P
Sbjct: 676 TTDHISPAGSIAVSSPAGQYLLAHGVAAGDFNSYGARRGNHEVMMRGTFANVRIRNLMLP 735

Query: 811 PTADGSREEGGVTVFQNEGALQGEKMFIFDAAMQYMAQGTPTVVFAGEEYGTGSSRDWAA 870
              DGSR EGG+T+ Q EG+    +M IFDAA +Y   G P++VFAG EYGTGSSRDWAA
Sbjct: 736 AKVDGSRVEGGLTLHQPEGS----EMPIFDAASRYQEAGIPSIVFAGTEYGTGSSRDWAA 791

Query: 871 KGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFKAGDSWETLGLTGNEVIDVLP-DPAL 929
           KG +LLG++AVVA+SFERIHRSNLVGMGVLPLQF+ G+S  +LG+ G+E   V      L
Sbjct: 792 KGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFHVRGLSGVL 851

Query: 930 TPQSDARLVIRRADGTVREVVVTLRIDTPIEVDYYRAGGILPFVLRQLL 978
            P+ +  L I    G  R + + LR+DT IE+DY   GGILP+VLR LL
Sbjct: 852 RPRQEVVLEIVNRQGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLL 900


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: 2358
Number of extensions: 109
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: 903
Length adjustment: 44
Effective length of query: 936
Effective length of database: 859
Effective search space:   804024
Effective search space used:   804024
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 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