GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Klebsiella michiganensis M5al

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate BWI76_RS00845 BWI76_RS00845 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:Q8U0B6
         (330 letters)



>FitnessBrowser__Koxy:BWI76_RS00845
          Length = 334

 Score =  185 bits (470), Expect = 1e-51
 Identities = 127/342 (37%), Positives = 183/342 (53%), Gaps = 29/342 (8%)

Query: 1   MIKAAVVGASGYIGGELVRLLAMHPEVEITAIT---SRQYAGKKVHKVHPNLRGL----- 52
           M+   +VGASGY G ELV  +  HP + ITA+T       AGK V  +HP L+G+     
Sbjct: 1   MLNTLIVGASGYAGAELVAYVNRHPHMTITALTVSAQSNDAGKLVSDLHPQLKGIVDLPL 60

Query: 53  -DLRFTNDYNFDADVIFLAVPHGTSMKIIEEFLGSAKII-DMSADFRIKK-ELYEKYYG- 108
             +   ++++   DV+FLA  H  S  +  +FL +  ++ D+S  FR+     YEKYYG 
Sbjct: 61  QPMSDISEFSAGVDVVFLATAHEVSHDLAPQFLAAGCVVFDLSGAFRVNDGAFYEKYYGF 120

Query: 109 PHEKPELIDRFTYGLPELHRKEIKKAELVANPGCNATATILGLYP-----FKDLTQEAIV 163
            H+ PEL+++  YGL E   +++K+A L+A PGC  TA  L L P       DL Q  ++
Sbjct: 121 THQHPELLEQAVYGLAEWSVEKLKEANLIAVPGCYPTAAQLSLKPLIDAGLLDLNQWPVI 180

Query: 164 DLKVSSSAGGRRENIASIHPERSNVVRVYKPYHHRHEAEVLQETRVKAMFTVHSVDLVRG 223
           +     S  GR+ +I +   E S  ++ Y  ++HRH  E+        +FT H  +  RG
Sbjct: 181 NATSGVSGAGRKASIGNSFCEVS--LQPYGVFNHRHHPEISTHLGADVIFTPHLGNFKRG 238

Query: 224 LLATIYFRYE-GNERELLRKLLM--YKDEPFVRIVTDKGGLQRYPDPKYVIGSNFIDIGF 280
           +L TI  R + G  +E +  +    Y D+P VR+  DKG     P  K V+G  F DIGF
Sbjct: 239 ILETITCRLKPGVSKEQVAAVFQQAYADKPLVRLY-DKG----VPALKNVVGLPFCDIGF 293

Query: 281 AYDSENSRVMVFSAIDNLIKGGAGQAVQNMNIMFGLKETTGL 322
           A   E+  ++V +A DNL+KG A QAVQ  NI FG  ET  L
Sbjct: 294 AVQDEH--IIVVAAEDNLLKGAAAQAVQCANIRFGFAETQSL 333


Lambda     K      H
   0.321    0.139    0.402 

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: 302
Number of extensions: 17
Number of successful extensions: 7
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: 330
Length of database: 334
Length adjustment: 28
Effective length of query: 302
Effective length of database: 306
Effective search space:    92412
Effective search space used:    92412
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 (21.8 bits)
S2: 49 (23.5 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