GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Herbaspirillum seropedicae SmR1

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate HSERO_RS05205 HSERO_RS05205 dihydroxy-acid dehydratase

Query= reanno::pseudo5_N2C3_1:AO356_28760
         (594 letters)



>FitnessBrowser__HerbieS:HSERO_RS05205
          Length = 585

 Score =  431 bits (1109), Expect = e-125
 Identities = 255/603 (42%), Positives = 347/603 (57%), Gaps = 42/603 (6%)

Query: 7   RRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTPCNRHHL 65
           R LRS  WF     AD        +M N G+   E Q G+P+IGI  T S+LTPCN H  
Sbjct: 10  RTLRSAGWFGT---ADKNGFMYRSWMKNQGIPDHEFQ-GKPVIGICNTWSELTPCNAHFR 65

Query: 66  ELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVLT 125
           ++A+ V+ GI +AGG P+EFPV    E + RPTA L RNLA + + E + G P+D VVL 
Sbjct: 66  KIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPIDAVVLL 125

Query: 126 TGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYE 185
           TGCDKTTPA LM AA+ D+PAIV++GGPML+G H+G  IGSGTV+W     + AGEI   
Sbjct: 126 TGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAGEITIH 185

Query: 186 GFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRI 245
            FM      S S G CNTMGTA +M  +AE+LG+SLP  A+IPA    R  +A+ +G RI
Sbjct: 186 DFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGMRI 245

Query: 246 CELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGE 305
            ++V + +  S+I+TR+AFENAI   +A+G S+N   HL AIA  +GV+L L+DW RIG 
Sbjct: 246 VDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDWTRIGR 305

Query: 306 DVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL-HEDCATVSGRTIGEIVSSSLT 364
             P +V+  P+G+YL E F+ AGG+P+V+  L +A  L H+D  TV+G+T+ + V  +  
Sbjct: 306 GTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNVKDAPI 365

Query: 365 SNADVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAENSFEARA 423
            N +V+ P   PL    G  +L GN     A++K S       K              RA
Sbjct: 366 YNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMK-----------HRGRA 414

Query: 424 IVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSLP 483
           +VFE    Y  RI+DP LD+D  C+LV++ VG  GYPG AEV NM  P  ++  G+  + 
Sbjct: 415 VVFEDFNHYKERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMV 474

Query: 484 CLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRR 543
            + D R SGT+    IL+++PEAA GG L ++Q  D +++D     + L I +EEM +RR
Sbjct: 475 RISDARMSGTAYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEM-KRR 533

Query: 544 LEWTPNIPPSQTP-----WQELYRQLVGQLSTG-------GCLEPATLHLRVIARSGEPR 591
           LE    +   + P     +Q LY   V Q   G       GC   A            P+
Sbjct: 534 LEARAKVLAERKPEMVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAV-----------PK 582

Query: 592 HSH 594
           HSH
Sbjct: 583 HSH 585


Lambda     K      H
   0.319    0.135    0.407 

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: 954
Number of extensions: 65
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 594
Length of database: 585
Length adjustment: 37
Effective length of query: 557
Effective length of database: 548
Effective search space:   305236
Effective search space used:   305236
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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