Alignments for a candidate for agx1 in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Klebsiella michiganensis M5al

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate BWI76_RS10590 BWI76_RS10590 class V aminotransferase

Query= BRENDA::P21549
         (392 letters)



>FitnessBrowser__Koxy:BWI76_RS10590
          Length = 413

 Score =  213 bits (543), Expect = 6e-60
 Identities = 130/385 (33%), Positives = 199/385 (51%), Gaps = 20/385 (5%)

Query: 18  LSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLV 77
           L+ P++LL+GPGP N  PR++ A   Q+IG     M   M+E+    + VF+T N  T++
Sbjct: 9   LNPPSRLLMGPGPINADPRVLRAMSSQLIGQYDPAMTHYMNEVMALYRGVFRTENRWTML 68

Query: 78  ISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQ 137
           + G+    +EA LV+ + PGD  LV   G +G    +I  R  A VH +    G  +T  
Sbjct: 69  VDGTSRAGIEAILVSAIRPGDKVLVPVFGRFGHLLCEIARRCRAEVHTIEVPWGEVFTPD 128

Query: 138 EVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDR 197
           +VE+ + + +P LL    G++ST +LQPL   GE+C RY  L   D+ ASLGG PL  D 
Sbjct: 129 QVEDAVKRIRPRLLLTVQGDTSTTMLQPLAELGEICRRYDALFYTDATASLGGNPLETDV 188

Query: 198 QGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKP----------------FSFY 241
            G+D + +G QK L  P GTS I+ S + ++ +  RK                   +S Y
Sbjct: 189 WGLDAVSAGMQKCLGGPSGTSPITLSARMEEAIRRRKCVEEGIRTDAHRDGDEEMIYSNY 248

Query: 242 LDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGR 301
            D+  + ++WG +   R+ HHT    +L+  RE   LI ++GL+    +H+     L   
Sbjct: 249 FDLGMVMDYWGPE---RLNHHTEATTALFGARECARLILQEGLDYGIARHKLHGDALVKG 305

Query: 302 LQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRI 361
           +QA+GL+ F  D   ++  V  V +P G +       +++ F IEI    GP  GKV RI
Sbjct: 306 IQAMGLETF-GDLKHKMNNVLGVVIPQGINGDQARKLMLEDFGIEIGTSFGPLHGKVWRI 364

Query: 362 GLLGCNATRENVDRVTEALRAALQH 386
           G +G NA ++ V     AL + L +
Sbjct: 365 GTMGYNARKDCVMTTLSALESVLNY 389


Lambda     K      H
   0.320    0.138    0.421 

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: 404
Number of extensions: 20
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: 392
Length of database: 413
Length adjustment: 31
Effective length of query: 361
Effective length of database: 382
Effective search space:   137902
Effective search space used:   137902
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 Aug 03 2021. The underlying query database was built on Aug 03 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis