GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011386009.1
          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:

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