GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Pseudomonas stutzeri RCH2

Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate GFF1981 Psest_2024 isocitrate dehydrogenase, NADP-dependent, prokaryotic type

Query= BRENDA::Q4J6C9
         (411 letters)



>FitnessBrowser__psRCH2:GFF1981
          Length = 418

 Score =  366 bits (939), Expect = e-106
 Identities = 193/410 (47%), Positives = 269/410 (65%), Gaps = 9/410 (2%)

Query: 8   PQDGEPIKFEKGKWV-VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWL 66
           P  G+ I       + VPN PII YIEGDGIG +I+   I+VV+ AV+KAY   R+I W+
Sbjct: 9   PSSGDKITVNADNTLNVPNNPIIPYIEGDGIGVDISPVMIKVVDAAVQKAYGGQRKIAWM 68

Query: 67  EVYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYA 124
           E+YAGEKA ++       PKET + +  Y V +KGPL TP+G G +S+NVA+R  LDLY 
Sbjct: 69  EIYAGEKATQVYDQDTWLPKETLEAVRDYVVSIKGPLTTPVGGGIRSLNVALRQELDLYV 128

Query: 125 NIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL--- 181
             RPV++  G+ SP+K P  VDM+IFREN++D+Y G+E+   S EA+K+ KFL EE+   
Sbjct: 129 CQRPVRWFTGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKFLTEEMGVK 188

Query: 182 KVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAY 241
           K+   ++ GIG+K +S   T+R+ R AL YA+ N R  VT++HKGN+MK+TEG+F+EW Y
Sbjct: 189 KIRFTENCGIGIKPVSLEGTKRLVRKALQYAVDNDRSSVTIVHKGNIMKFTEGAFKEWGY 248

Query: 242 EVALNEYRDKIVTEEEIN--RGVNSEGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNG 299
           EVA +E+  +++        +  N+   +++ D IAD MLQQI++RP EYD+I   N+NG
Sbjct: 249 EVARDEFGAELLDGGPWMQFKNPNTGKNIVVKDAIADAMLQQILLRPAEYDVIATLNLNG 308

Query: 300 DYISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYF 359
           DY+SDA  A +G IG+  GAN+ DT  MFEA HGTAPKYAG++  NP  +I S E+ML  
Sbjct: 309 DYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGQDKVNPGSLILSAEMMLRH 368

Query: 360 MGWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408
           MGW EAA LI K+   +I  K VT D  R + G   +   ++ D ++  M
Sbjct: 369 MGWVEAADLIIKSTESAIAAKTVTYDFERLMEGAQLMSCSQFGDAMISHM 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: 500
Number of extensions: 21
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