GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Azospirillum brasilense Sp245

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate AZOBR_RS31260 AZOBR_RS31260 dihydroxy-acid dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1668
         (594 letters)



>FitnessBrowser__azobra:AZOBR_RS31260
          Length = 608

 Score =  767 bits (1981), Expect = 0.0
 Identities = 380/608 (62%), Positives = 464/608 (76%), Gaps = 14/608 (2%)

Query: 1   MSDT---PKH-------RLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGI 50
           MSDT   P+H       RLRS  WF++P + DMTALY+ERY+N+G+TREELQSG PIIGI
Sbjct: 1   MSDTKPSPQHPEIGSGRRLRSRAWFDNPDNPDMTALYLERYLNFGLTREELQSGAPIIGI 60

Query: 51  AQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGL 110
           AQTGSDL+PCNRHHL LA+R++ GIR AGGI +EFPVHPI E  +RPTA++DRNLAYLGL
Sbjct: 61  AQTGSDLSPCNRHHLVLAERLREGIRTAGGIAIEFPVHPIQETGKRPTASIDRNLAYLGL 120

Query: 111 VEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVL 170
           VE+LHGYPLDGVVLT GCDKTTPACLMAAAT ++PAI LS GPML+G  +GE  GSGT++
Sbjct: 121 VEVLHGYPLDGVVLTIGCDKTTPACLMAAATVNIPAIALSVGPMLNGWFRGERTGSGTIV 180

Query: 171 WHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAP 230
           W AR +MAAGEIDY+GF+E+  +++PS G+CNTMGTA +MN+LAE LGM LPG A+IPAP
Sbjct: 181 WKARQMMAAGEIDYQGFIELVASSAPSTGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAP 240

Query: 231 YRERGQMAYATGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARH 290
           YRER Q  Y TGKRI ++VR+D++PS I+TR AF NAI V SA+G S+N P H+ AIA+H
Sbjct: 241 YRERQQADYETGKRIVEMVREDLKPSDILTRDAFLNAIVVNSAIGGSTNAPIHINAIAKH 300

Query: 291 MGVELSLEDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATV 350
           +GV L++EDWQ  G DVPLLVN  PAG+YLGE FHRAGGVP+V+ +L   G + E   TV
Sbjct: 301 IGVPLTVEDWQTHGHDVPLLVNLQPAGEYLGEDFHRAGGVPAVVAQLMGKGLIREGAPTV 360

Query: 351 SGKTIGEIVSNSLTSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYL 410
           +G+TIGE        +T VIHP D PL   AGF+VL GN F +AIMK SV+ + FR+ YL
Sbjct: 361 NGRTIGENCRRQPILDTRVIHPIDEPLMPNAGFVVLRGNLFGAAIMKTSVISDEFRERYL 420

Query: 411 SEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAP 470
           S P    +FE + +VF+GPEDYH RIDDP+L ID   ILVIRG G +GYPG+AEVVNM P
Sbjct: 421 SNPQDPEAFEGKVVVFDGPEDYHHRIDDPSLGIDAYTILVIRGTGPIGYPGAAEVVNMRP 480

Query: 471 PAALIKQGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTV 530
           PA LIKQG+ SLPC+GDGRQSGTS SPSILN SPEAA GGGLALL++ DR+++DL   + 
Sbjct: 481 PATLIKQGVHSLPCIGDGRQSGTSGSPSILNASPEAAAGGGLALLRSGDRVRIDLRRGSA 540

Query: 531 NLLIDDAEMAQRRREWIP----NIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIAR 586
           ++LI + E+A RR          IPPSQTPWQE+ R +V QL  G  L+PA  + RV   
Sbjct: 541 DILIPEGELADRRAALEAAGGYPIPPSQTPWQEIQRGIVDQLDEGMVLKPAVKYQRVAQT 600

Query: 587 SGEPRHSH 594
            G PR +H
Sbjct: 601 MGIPRDNH 608


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: 1191
Number of extensions: 56
Number of successful extensions: 2
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: 608
Length adjustment: 37
Effective length of query: 557
Effective length of database: 571
Effective search space:   318047
Effective search space used:   318047
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