GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Collimonas arenae Ter10

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_061535420.1 CAter10_RS16755 acetylornithine transaminase

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



>NCBI__GCF_001584165.1:WP_061535420.1
          Length = 400

 Score =  171 bits (432), Expect = 5e-47
 Identities = 135/421 (32%), Positives = 208/421 (49%), Gaps = 61/421 (14%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY--AFNAA 72
           P+    G    + D  GKRY+D++ G  V  LGH    + +A+ AQ+ ++ +   AF  A
Sbjct: 19  PLVFVEGDGMWMTDHTGKRYLDYLQGWAVNALGHSPQCIQDALVAQSKKIINPSPAFYNA 78

Query: 73  PHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR---------GATGKRAII 123
           P      L+   S F  V +      TNSGAEA E A+K+AR             +  II
Sbjct: 79  PSIELANLLTANSCFDRVFF------TNSGAEANEGAIKLARKWGKKNPNKAGQNRFEII 132

Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183
            F+  FHGRTLAT++ +GK         ++PG      +P A+           ++ L S
Sbjct: 133 TFNHSFHGRTLATMSASGKPGWDTIFAPQVPG------FPKAE-----------LNDLAS 175

Query: 184 VELAVED-VAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242
           VE  + D   A + EPVQGE G +     F QALR    + GIL+I+DE+QSG GRTG+ 
Sbjct: 176 VENLINDKTVAVMLEPVQGESGVIPATREFMQALRELTKKHGILLIVDEVQSGMGRTGEL 235

Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS 302
           FA+   GIEPD++ L K I GG+PL A++ R+E+ A    G  GGTY+GNP+  A  +A 
Sbjct: 236 FAYQLSGIEPDIMTLGKGIGGGVPLAALLAREEI-AVFEAGDQGGTYNGNPLMTAVGVAV 294

Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPA 362
           +  + +           Q++     + K + LS  + +LT   A  G+E    +G     
Sbjct: 295 IKTLLEPGFL-------QSV-----KDKGAYLSSELLKLT---AKHGLEGERGEGLLRAL 339

Query: 363 QLAK-----VMEAAR---ARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
           +L K     +++ AR     GLLL  +    +++R +  L +    +++ + +L   L +
Sbjct: 340 KLGKDIGPQIVDIARDLNPVGLLL--NSPRPNLLRFMPSLNVTTAEIDQMIAMLSDVLTQ 397

Query: 415 L 415
           L
Sbjct: 398 L 398


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: 409
Number of extensions: 17
Number of successful extensions: 5
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: 400
Length adjustment: 31
Effective length of query: 385
Effective length of database: 369
Effective search space:   142065
Effective search space used:   142065
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 24 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