GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Flavobacterium glycines Gm-149

Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_066324960.1 BLR17_RS07090 aconitate hydratase

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_900100165.1:WP_066324960.1
          Length = 753

 Score =  183 bits (465), Expect = 1e-50
 Identities = 136/418 (32%), Positives = 196/418 (46%), Gaps = 41/418 (9%)

Query: 29  DQIALQDGTAPLAIRQLMELGTEVRAADRT----HFFVDHAAPSPRRELSNDQK-----F 79
           D++A QD TA +A+ Q M  G    A   T    H        S    ++N Q      F
Sbjct: 62  DRVACQDATAQMALLQFMHAGKSKVAVPTTVHCDHLIQAKVGASTDLAVANTQSKEVFDF 121

Query: 80  IYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSHTCTYGGIGAFSTGMGSTDV 139
           +   + K G  F  PG GIIHQI++E Y  PG + +G DSHT   GG+G  + G+G  D 
Sbjct: 122 LSSVSNKYGIGFWKPGSGIIHQIVLENYAFPGGMMIGTDSHTVNAGGLGMLAIGVGGAD- 180

Query: 140 AVAIALGKNW-FRVPESFRVQLDGSLPKGVFAKDVILKLIGDLGVDGATYKALEFHGECA 198
           AV +  G +W  + P+   V+L G L      KDVILK+   L V G T   +E+ GE A
Sbjct: 181 AVDVMSGMSWELKFPKLIGVKLTGKLSGWTAPKDVILKVADILTVKGGTGAIVEYFGEGA 240

Query: 199 ENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDF-------------REV 245
            NM+   + TI NM  E GA    F  D++ R++L   GR+                 EV
Sbjct: 241 TNMSCTGKGTICNMGAEIGATTSTFGYDDSMRRYLTATGRQDVVDAADKVAAYLTADSEV 300

Query: 246 KADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEG--------TEVNQVYIGTCT 297
            A+ +  +++ I +++S L P ++ P   D    +S+++          +V    IG+CT
Sbjct: 301 YANPEQYFDQLIEINLSELEPHINGPFTPDRGTPVSQMKAEAEANGWPLKVEWGLIGSCT 360

Query: 298 NGRLSDLEVAARILKGRKVKEGV----RLIVVPASRRVYLQALDKGLIRVFVEAGGMVLN 353
           N    D+  AA I++ + V  GV       + P S ++       G+I  F + G  V  
Sbjct: 361 NSSYEDMSRAASIVR-QAVALGVTPKAEFGINPGSEQIRYTIERDGIIADFEKMGTKVFT 419

Query: 354 PGCGPCVGIHQGILAD-GE--VCISTQNRNFKGRM-GNPNAEIFLASPATAAASAVKG 407
             CGPC+G      AD GE    + + NRNF  R  GNPN   F+ SP   AA A+ G
Sbjct: 420 NACGPCIGQWDRAGADKGEKNTIVHSFNRNFSKRADGNPNTHAFVTSPEMVAALAISG 477


Lambda     K      H
   0.318    0.136    0.391 

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: 731
Number of extensions: 46
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: 753
Length adjustment: 36
Effective length of query: 380
Effective length of database: 717
Effective search space:   272460
Effective search space used:   272460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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