GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Klebsiella michiganensis M5al

Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate BWI76_RS11330 BWI76_RS11330 isocitrate dehydrogenase (NADP(+))

Query= BRENDA::Q4J6C9
         (411 letters)



>FitnessBrowser__Koxy:BWI76_RS11330
          Length = 416

 Score =  387 bits (995), Expect = e-112
 Identities = 197/409 (48%), Positives = 275/409 (67%), Gaps = 8/409 (1%)

Query: 8   PQDGEPIKFEKGKWVVPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLE 67
           P +G+ I  + GK  VPN PII +IEGDGIG ++T + ++VV+ AVEKAYK  R+I W+E
Sbjct: 8   PAEGQKITLQNGKLNVPNNPIIPFIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWME 67

Query: 68  VYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYAN 125
           VY GEK+ ++ G     P ET D++ +YRV +KGPL TP+G G +S+NVA+R  LDLY  
Sbjct: 68  VYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYVC 127

Query: 126 IRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---K 182
           +RPV+Y +G  SP+KHPE  DM+IFREN++D+Y GIE+  DS EA K+ KFLR+E+   K
Sbjct: 128 LRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSAEADKVIKFLRDEMGVKK 187

Query: 183 VDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYE 242
           +   +  GIG+K  S+  T+R+ R A+ YA+ N R  +T++HKGN+MK+TEG+F++W Y+
Sbjct: 188 IRFPEHCGIGIKPCSEEGTKRLVRAAIEYAITNDRDSLTLVHKGNIMKFTEGAFKDWGYQ 247

Query: 243 VALNEYRDKIVTEEEINR--GVNSEGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGD 300
           +A  E+  +++      +    N+  ++++ D IAD  LQQI++RP EYD+I   N+NGD
Sbjct: 248 LAREEFGGELIDGGPWLKIKNPNTGKEIVVKDVIADAFLQQILLRPAEYDVIACMNLNGD 307

Query: 301 YISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFM 360
           YISDA  A +G IG+  GANIGD   +FEA HGTAPKYAG++  NP  II S E+ML  M
Sbjct: 308 YISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHM 367

Query: 361 GWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408
            W EAA LI K    +I  K VT D  R + G   L   E+ D ++  M
Sbjct: 368 QWFEAADLIVKGTEGAIAAKTVTYDFERLMEGAKLLKCSEFGDAIIANM 416


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: 519
Number of extensions: 18
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: 416
Length adjustment: 31
Effective length of query: 380
Effective length of database: 385
Effective search space:   146300
Effective search space used:   146300
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