GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Magnetospirillum magneticum AMB-1

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase

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



>NCBI__GCF_000009985.1:WP_011383255.1
          Length = 388

 Score =  176 bits (445), Expect = 1e-48
 Identities = 130/405 (32%), Positives = 206/405 (50%), Gaps = 47/405 (11%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           +    G  A +  +DG+R++DF  G+ V  LGH +P +V A++AQA +L H +      G
Sbjct: 15  VIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPG 74

Query: 76  PYLALMEQLSQ-FVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGG 128
                 E++++  +  S+       N+GAEA E  +K+AR      G   +  I+A  G 
Sbjct: 75  -----QERVAERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGS 129

Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188
           FHGRT+ATL   G    Y +  G +     H+PY         E A  A+          
Sbjct: 130 FHGRTIATLAAAG-TPKYLEGFGPVAQGFDHVPYGDL------EAARGAIG--------- 173

Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
            + AA + EPVQGEGG    DPA+ + LR   D+ G+L+++DE+Q+G GRTG+ FA    
Sbjct: 174 SNTAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWS 233

Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308
           GI PD++ LAK + GG P+GAV+  ++  + +  G  G T+ GNP++ A A A L    D
Sbjct: 234 GIAPDVMGLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVL----D 289

Query: 309 ENLATWGERQEQAIVSRYERWKASGLS----PYIGRLTGVGAMRGIEFANADGSPAPAQL 364
           E +A     + QA+ +   R +   L+      I ++ G G M G++       P   + 
Sbjct: 290 EVMAPGFLERVQAVAALL-RGRLDDLARRYPGAIAQVRGQGLMLGLKTV-----PVNTEF 343

Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILE 409
              + AA   GLL + +G   +++RL+ PL I    +E  ++I++
Sbjct: 344 NAKLFAA---GLLAVGAGD--NVVRLVPPLIIGEAEVERAVEIID 383


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: 457
Number of extensions: 24
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: 388
Length adjustment: 31
Effective length of query: 385
Effective length of database: 357
Effective search space:   137445
Effective search space used:   137445
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