GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Pseudomonas litoralis 2SM5

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein

Query= BRENDA::P9WQ77
         (449 letters)



>NCBI__GCF_900105005.1:WP_090273343.1
          Length = 404

 Score =  140 bits (352), Expect = 1e-37
 Identities = 135/414 (32%), Positives = 194/414 (46%), Gaps = 52/414 (12%)

Query: 41  RSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYS 100
           R  GS L D   GR Y+D+   +A ++LG   P LV+     A+ +    N  +N     
Sbjct: 29  RGDGSRLWDQ-QGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVSNIMTNEPALR 87

Query: 101 VAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQV 160
           +A      TFA          + FV  GA A E A K A  W   H+Q+ G D     ++
Sbjct: 88  LADKLVAATFA--------DKVLFVNSGAEANEAAFKLARRWA--HDQS-GPDKH---EI 133

Query: 161 LHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQ 220
           +    +FHGR+ +T+S+   +P  +  F     P I      P  D   +AALEA+   +
Sbjct: 134 IACSNSFHGRTLFTVSVGG-QPKYSQGFG----PAISGISHVPYND---IAALEAQISER 185

Query: 221 ARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLT 280
             A            V EP+QGEGG      E+  A+R LCD+++ALLIFDEVQ+G G T
Sbjct: 186 TCAV-----------VVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRT 234

Query: 281 GTAWAYQQLDVAPDIVAFGKKTQVCG---VMAGRRVDEVADNVFAVPSRLNSTWGGNLTD 337
           G  +AY    VAPDI+   K   + G   + A   +D VA  +        ST+GGN   
Sbjct: 235 GKLYAYMHSGVAPDILTSAK--GIGGGFPIAAMLTIDRVAPALSV--GTHGSTYGGNPLG 290

Query: 338 MVRARRILEVIEA----EGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSL 393
              A R+L++I      +G+ ER  Q    LR   DEL      V  + RG+GL+    L
Sbjct: 291 CAVAERVLDIINTPQVLDGVGERQAQLTAGLRILADEL-----GVFSEIRGQGLLIGAVL 345

Query: 394 PT--TADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSAL 445
                    +++R   +  ++VL AGAD VR  P L +  A+I  A+  +R+AL
Sbjct: 346 AERWRGQAGQVMRLAQEEGLLVLQAGADVVRLAPSLIIPEADIREALGRMRAAL 399


Lambda     K      H
   0.323    0.137    0.412 

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: 383
Number of extensions: 23
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: 449
Length of database: 404
Length adjustment: 32
Effective length of query: 417
Effective length of database: 372
Effective search space:   155124
Effective search space used:   155124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 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