GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Burkholderia phytofirmans PsJN

Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate BPHYT_RS15730 BPHYT_RS15730 isocitrate dehydrogenase

Query= BRENDA::Q4J6C9
         (411 letters)



>FitnessBrowser__BFirm:BPHYT_RS15730
          Length = 418

 Score =  382 bits (980), Expect = e-110
 Identities = 194/394 (49%), Positives = 277/394 (70%), Gaps = 8/394 (2%)

Query: 23  VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLEVYAGEKANKITGDR- 81
           V ++PII YIEGDG G +IT   I+VV+ AVEKAY   ++I W+E+YAGEK+ K+ G   
Sbjct: 25  VSDQPIIPYIEGDGTGLDITPVMIKVVDAAVEKAYAGKKKIHWMEIYAGEKSTKVYGPDV 84

Query: 82  -FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYANIRPVKYIEGLESPLK 140
             P+ET  +L +Y V +KGPL TP+G G +S+NVA+R  LDLY  +RPV+Y +G+ SP++
Sbjct: 85  WLPEETLQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPVQYFKGVPSPVR 144

Query: 141 HPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---KVDIEDDTGIGLKVMS 197
            PEK +M+IFREN++D+Y GIE+P +SE+AKK+ KFLREE+   K+   D +GIG+K +S
Sbjct: 145 EPEKTNMVIFRENSEDIYAGIEWPAESEQAKKVIKFLREEMGVKKIRFPDTSGIGIKPVS 204

Query: 198 KFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYEVALNEYRDKIVTEEE 257
           +  T+R+ R A+ YA+ N R+ VT++HKGN+MK+TEG+FR++ Y +A  E+  +++    
Sbjct: 205 REGTERLVRKAIQYAIDNERRSVTLVHKGNIMKFTEGAFRDYGYALAQKEFAAELIDGGP 264

Query: 258 INRGVNSE--GKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGM 315
             +  N +  G ++L D IAD  LQQI++RP EYD+I   N+NGDY+SDA  A +G IG+
Sbjct: 265 WMKIKNPKTGGDIVLKDVIADAFLQQILLRPAEYDVIATLNLNGDYVSDALAAQVGGIGI 324

Query: 316 LGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEAARLIEKAINE 375
             GAN+ D+  MFEA HGTAPKYAGK+  NP   I S E+ML  +GW+EAA LI K++ +
Sbjct: 325 APGANMSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHLGWTEAADLIIKSMEK 384

Query: 376 SIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408
           SI QK+VT D AR + G T +    +   L++ M
Sbjct: 385 SILQKRVTYDFARLMEGATQVSCSGFGQVLIENM 418


Lambda     K      H
   0.317    0.137    0.394 

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: 517
Number of extensions: 22
Number of successful extensions: 4
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: 411
Length of database: 418
Length adjustment: 31
Effective length of query: 380
Effective length of database: 387
Effective search space:   147060
Effective search space used:   147060
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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