GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Methylocystis bryophila S285

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_245300308.1 B1812_RS21480 diaminobutyrate--2-oxoglutarate transaminase

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



>NCBI__GCF_002117405.1:WP_245300308.1
          Length = 454

 Score =  184 bits (468), Expect = 4e-51
 Identities = 135/412 (32%), Positives = 198/412 (48%), Gaps = 31/412 (7%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           PI L  G    V D + + YID + G G   LGH +  VV+A++   +          P 
Sbjct: 31  PIALKSGGGVRVRDVEDREYIDCLSGAGTQPLGHNHEVVVDAVRDALSGAVPLQTLDLPT 90

Query: 75  GPYLALMEQLSQFVPVSYPLAGMLT---NSGAEAAENALKVARGATGKRAIIAFDGGFHG 131
                 +  L   +P  +P    +     SGA+A E ALK+ R ATG+R I++F G +HG
Sbjct: 91  PLKDRFIGDLFDSLPAEFPNNFKIQFCGPSGADAIEAALKLVRTATGRRGILSFRGAYHG 150

Query: 132 RTLATLNLNGKVAPYKQRVGELPGPVYHLPYPS-------ADTGVTCEQALKAMDRLFSV 184
            T   L+L G+  P K  +      V  LPYPS              E + + ++ L   
Sbjct: 151 MTSGALSLTGESGP-KAAINGGAAEVQFLPYPSDYRCPFGLGGHAGSEMSARYIENLLED 209

Query: 185 ELA-VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243
            L+ V   AA I E VQGEGG      ++ + +R   + RGI +I+DE+Q+G GRTG+ +
Sbjct: 210 PLSGVPLPAAMILEVVQGEGGINPAPDSWLRKIREITEFRGIPLILDEVQTGLGRTGRLY 269

Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303
           AF   GI PD+L+L+K+I GG+PL  V+ R+EL    P G   GT+ GN ++ AA  A++
Sbjct: 270 AFQHAGITPDVLVLSKAIGGGLPLSVVIYRRELDHWQP-GAHAGTFRGNQLAFAAGAATI 328

Query: 304 ----AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANAD--- 356
               AQ  + N    G R + A+ S     +       IG + G G M G+E   AD   
Sbjct: 329 RFISAQRLECNAEEMGCRLQDALRSIQSETRC------IGHVRGRGLMVGVEIVRADHTD 382

Query: 357 -----GSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEE 403
                 S +P    K+      RGL+L   G+   +IR L PL +    ++E
Sbjct: 383 RLAGPPSSSPQMAQKLQNECLRRGLILERGGRLGSVIRFLPPLIVTPAEIDE 434


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: 503
Number of extensions: 24
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: 454
Length adjustment: 32
Effective length of query: 384
Effective length of database: 422
Effective search space:   162048
Effective search space used:   162048
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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