GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Methanospirillum lacunae Ki8-1

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase

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



>NCBI__GCF_003173355.1:WP_109969613.1
          Length = 384

 Score =  207 bits (528), Expect = 3e-58
 Identities = 145/407 (35%), Positives = 207/407 (50%), Gaps = 47/407 (11%)

Query: 11  AIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-F 69
           A    I ++ G    V D DGK+Y+D V GI V + GHC+P VV+AI  QA  L H +  
Sbjct: 18  AFSREIMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNL 77

Query: 70  NAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGF 129
              PH    AL ++L +   +        +NSGAEA E ALK+AR  TG++  IA +GGF
Sbjct: 78  FYVPHQG--ALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLARIRTGRKEFIACEGGF 135

Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189
           HGRT+ +L    K A  +  +   P   + +PY          QALK            E
Sbjct: 136 HGRTMGSLACTHKPAIREPFMPLQPFTSF-VPYGDV-------QALKGA--------ITE 179

Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249
           + AA I EP+QGEGG +   P + + +R  CD +G+L+I+DE+QSG GRTG  FAF   G
Sbjct: 180 ETAAVILEPIQGEGGVIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEG 239

Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD- 308
           I PD++ +AK++A G P+GA+V R+ L     K   G T++G PI+CAAALAS+  +   
Sbjct: 240 IHPDIITMAKAMASGFPMGAIVAREGL--EFGKSEHGSTFAGGPIACAAALASIDVIGKV 297

Query: 309 -ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367
              +A  GER   A+     R K              G M GI   +          A V
Sbjct: 298 LPEVAAKGERFRAALAHLNPRVK--------------GLMIGITIGD--------HCADV 335

Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
            +     GLL+  +  A   +RL+ PLTI    +++   I+   +++
Sbjct: 336 QKECAVHGLLV--NCAAHGNLRLVPPLTITNAEIDKATGIINAAVSK 380


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: 456
Number of extensions: 29
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: 384
Length adjustment: 31
Effective length of query: 385
Effective length of database: 353
Effective search space:   135905
Effective search space used:   135905
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