GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase

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



>NCBI__GCF_001592305.1:WP_068170823.1
          Length = 428

 Score =  340 bits (873), Expect = 4e-98
 Identities = 175/411 (42%), Positives = 249/411 (60%), Gaps = 4/411 (0%)

Query: 4   ESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63
           ++  + + ++    + H +NAE+WD +G+R+IDF GGI VLN GH +P V  AI AQ  R
Sbjct: 19  DATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQAAIAAQLQR 78

Query: 64  LTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAII 123
            TH  +   P+  Y++L E+++  VP+         ++GAEA ENA+K+AR +TG+  +I
Sbjct: 79  FTHSCYQVVPYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIARSSTGRSGVI 138

Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183
           AF G FHGR+L  ++L GKV PYK   G  P  +YH+P+P+   G + ++  +AMD +F 
Sbjct: 139 AFGGAFHGRSLFAVSLTGKVQPYKAGFGPFPPEIYHVPFPA--EGASLDETKRAMDHVFK 196

Query: 184 VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243
            ++    VAA +FEPVQGEGGF  +       LR  CD+ GIL+I DE+Q+GF RTG+ F
Sbjct: 197 CDIEPSRVAAIVFEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQTGFARTGRMF 256

Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303
           A    G+ PDL+ +AKS+AGG  L AV G+  +M     GGLGGTY+GNP++ AA+ A L
Sbjct: 257 AMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNPLAIAASHAVL 316

Query: 304 AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363
             M +E L    +R    +V+     KA    P IG + G+GAM   EF +A G+P    
Sbjct: 317 DVMAEEKLPERAQRLGDQLVAHLRAAKAK--YPRIGEVRGLGAMVACEFVDAAGAPDADT 374

Query: 364 LAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
             +V  AA  RGLLL+  G   ++IR L PLTIE  V  E L +L+  +AE
Sbjct: 375 TKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAE 425


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: 547
Number of extensions: 15
Number of successful extensions: 3
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: 428
Length adjustment: 32
Effective length of query: 384
Effective length of database: 396
Effective search space:   152064
Effective search space used:   152064
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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