GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Klebsiella michiganensis M5al

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__Koxy:BWI76_RS11670
          Length = 406

 Score =  198 bits (503), Expect = 3e-55
 Identities = 133/401 (33%), Positives = 193/401 (48%), Gaps = 46/401 (11%)

Query: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80
           G  + +WD  GK YIDF GGI V  LGH +P +V+A+  QA +  H   N   + P L L
Sbjct: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG-NGYTNEPVLRL 86

Query: 81  MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGRTL 134
            +QL   +  ++       NSGAEA E ALK+AR        + K  I+AF   FHGRTL
Sbjct: 87  AKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTL 143

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAF 194
            T++  G+ A Y Q    LP  + H  Y   D+                  L  ++  A 
Sbjct: 144 FTVSAGGQPA-YSQDFAPLPPQIQHAIYNDLDSAKA---------------LIDDNTCAV 187

Query: 195 IFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDL 254
           I EP+QGEGG +  D  F + LR  CD    L+I DE+Q+G GRTG+ +A+   G+ PDL
Sbjct: 188 IVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDL 247

Query: 255 LLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATW 314
           L  AK++ GG P+GA++  +   + +  G  G TY GNP++CA A         E  AT 
Sbjct: 248 LSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVA--------GEVFATI 299

Query: 315 GERQEQAIVSRYERWKASGLSPYIGR------LTGVGAMRGIEFANADGSPAPAQLAKVM 368
             R+    V +  +W    L+    R      + G+G + G    +     A A    + 
Sbjct: 300 NTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKA----IS 355

Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILE 409
             A   GL+++ +G   +++R    L I  + +  GLD  E
Sbjct: 356 NQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGLDRFE 394


Lambda     K      H
   0.320    0.137    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: 412
Number of extensions: 17
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: 416
Length of database: 406
Length adjustment: 31
Effective length of query: 385
Effective length of database: 375
Effective search space:   144375
Effective search space used:   144375
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: 50 (23.9 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