GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ilvE in Pseudomonas simiae WCS417

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate GFF3889 PS417_19910 aromatic amino acid aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>lcl|FitnessBrowser__WCS417:GFF3889 PS417_19910 aromatic amino acid
           aminotransferase
          Length = 397

 Score =  324 bits (831), Expect = 2e-93
 Identities = 175/395 (44%), Positives = 241/395 (61%), Gaps = 2/395 (0%)

Query: 2   FQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPH 61
           F  +    GDPIL LM+ + +D   +K +L +G+Y ++ G+ P   +V  AE RL     
Sbjct: 3   FDAIGRVPGDPILGLMDLYAQDTNPNKFDLGVGVYKDDQGLTPIPHSVKLAEQRL-VDTQ 61

Query: 62  GASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPE 121
               Y+   G   +   I+ L+ GAD  +++++R    QT GG+GAL++ ADF+    P 
Sbjct: 62  TTKTYIGGHGNAAFGKLISELVLGADSTLIRERRAGATQTPGGTGALRLSADFIAHNLPG 121

Query: 122 SGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPC 181
            GVW+S+PTW  H  IFA AG  VS YP Y  A N +    +LATL T+P   +VLLH C
Sbjct: 122 RGVWLSNPTWPIHETIFAKAGIPVSHYP-YVGADNRLDVAAMLATLSTVPKGDVVLLHAC 180

Query: 182 CHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALV 241
           CHNPTG DL+ D W  V++I++ R+L+P +D AYQGFG G+E+DA+A+R  A+     LV
Sbjct: 181 CHNPTGFDLSQDDWRQVLQIVRERQLLPLIDFAYQGFGDGLEQDAWAVRLFAAELPEVLV 240

Query: 242 SNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLND 301
           ++S SK F LY +RVG L V   DAE    V  QL  T R  +S+PP+ GA VVA +L D
Sbjct: 241 TSSCSKNFGLYSDRVGALIVCAADAEKLTDVRSQLANTARNLWSTPPDHGAAVVATILGD 300

Query: 302 EALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDR 361
             LK  W  EVE MR+RI  +R  LV+ L+       F ++  QRGMFSYTGLSA QV +
Sbjct: 301 AELKKRWSDEVEAMRSRIAHLRSGLVEALAPHGLSARFAHIGAQRGMFSYTGLSAEQVKQ 360

Query: 362 LREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396
           LRE+  VY+++SGR  VAG++   +  +AKA A V
Sbjct: 361 LREKHSVYMVSSGRANVAGIDATRLTLLAKAIADV 395


Lambda     K      H
   0.320    0.135    0.401 

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: 389
Number of extensions: 14
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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