GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Marinobacter adhaerens HP15

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase

Query= reanno::Smeli:SM_b20890
         (579 letters)



>FitnessBrowser__Marino:GFF612
          Length = 597

 Score =  259 bits (661), Expect = 3e-73
 Identities = 180/544 (33%), Positives = 277/544 (50%), Gaps = 59/544 (10%)

Query: 43  GRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPVFSTGES-TLRPTAMMF 101
           G+PII + N++++  P + HL+DL + V R +  AGG   EF   +  +   +    M++
Sbjct: 19  GKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTIAVDDGIAMGHDGMLY 78

Query: 102 ----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGK 157
               R + A  VE  +  +  D +V +  CDK TP +LM A  ++IP I VSGGPM  GK
Sbjct: 79  SLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGK 138

Query: 158 WRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALG 217
            +  +      +     +      S E+  + E+    + GSC  M TA++M  + EA+G
Sbjct: 139 TKLSE--HKLDLVDAMVIAADPNASDEQVEEYERNACPTCGSCSGMFTANSMNCLTEAIG 196

Query: 218 MTLSGNAAIPAVDARRRVISQLTGRRIVEMVKE-------DLKPSDILTKEAFENAIRVN 270
           + L GN ++ A  A R  +    GR+IVE  +         + P  I +  AFENA+ ++
Sbjct: 197 LALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASVLPLSIASMAAFENAMVMD 256

Query: 271 GAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQP-SGKYLMEEFYYAGGL 329
            A+GGSTN +LHLLA A   GV  +L++ D+L R VP +  + P S KY ME+ + AGG+
Sbjct: 257 IAMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKVAPNSPKYHMEDVHRAGGI 316

Query: 330 PVVIKAVAEMGLLHNDAITVSGDTI------WNDVKG----VVNY--------------- 364
             ++  +   GL++ D  TV   T+      W+ ++     VV +               
Sbjct: 317 MGILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEVVEFYKAGPAGIPTQTAFS 376

Query: 365 ------------NEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRA 412
                           I   E A +  GG+AVL GN+A  G V+K +     +   +G+A
Sbjct: 377 QSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLYGNIALDGCVVKTAGVDESIFVFEGKA 436

Query: 413 VVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLK-KGI-TD 470
            VFES +   A I  +++   E  +++++Y GP+G PGM E   M  P   LK KG+  D
Sbjct: 437 RVFESQDSAVAGILSDEVKPGE--VVIIRYEGPRGGPGMQE---MLYPTSYLKSKGLGKD 491

Query: 471 MIRISDARMSGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELAR 530
              ++D R SG   G  I H +PEAA GG + L+ENGD I +DIPNR++++ +   EL R
Sbjct: 492 CALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRIDIPNRSINVELDQHELDR 551

Query: 531 RRAA 534
           RR A
Sbjct: 552 RREA 555


Lambda     K      H
   0.318    0.135    0.402 

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: 867
Number of extensions: 48
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: 579
Length of database: 597
Length adjustment: 37
Effective length of query: 542
Effective length of database: 560
Effective search space:   303520
Effective search space used:   303520
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: 53 (25.0 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