Alignments for a candidate for ilvD in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Herbaspirillum autotrophicum IAM 14942

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_198155988.1 AKL27_RS16455 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_001189915.1:WP_198155988.1
          Length = 339

 Score =  614 bits (1583), Expect = e-180
 Identities = 293/339 (86%), Positives = 325/339 (95%)

Query: 1   MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60
           M+FN+RS+NITQG++RSPNRSMYYALGY+KEDFDKPM+G+ANGHSTITPCN+GLQ+LAD 
Sbjct: 1   MSFNRRSKNITQGISRSPNRSMYYALGYEKEDFDKPMIGVANGHSTITPCNSGLQKLADI 60

Query: 61  AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120
           AI +IK + ANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETA  GQWMDGVVVI
Sbjct: 61  AISSIKDAGANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAVNGQWMDGVVVI 120

Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180
           GGCDKNMPGGMIALARTNVPGIYVYGGTIKPG WKGKDLTIVS+FEAVGEF+AGRMSQED
Sbjct: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGKWKGKDLTIVSAFEAVGEFSAGRMSQED 180

Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240
           F+G+EKNACPS+GSCGGMYTANTMSSSFEALGM+L YSSTMANPD+EK  SAA+SA+VLV
Sbjct: 181 FDGIEKNACPSSGSCGGMYTANTMSSSFEALGMALFYSSTMANPDEEKTGSAAQSAKVLV 240

Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300
           EA+K+D+KPRDII RKSIENAV LIMATGGSTNAVLHYLAIAHAAEVEWTIDDFER+R+K
Sbjct: 241 EAVKRDLKPRDIINRKSIENAVTLIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERVRQK 300

Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHG 339
           VPV C+LKPSG+YVATDLHKAGGIP V+K+LL+AG+LHG
Sbjct: 301 VPVFCDLKPSGKYVATDLHKAGGIPAVLKVLLQAGLLHG 339


Lambda     K      H
   0.316    0.133    0.386 

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: 703
Number of extensions: 23
Number of successful extensions: 1
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: 557
Length of database: 339
Length adjustment: 32
Effective length of query: 525
Effective length of database: 307
Effective search space:   161175
Effective search space used:   161175
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 (21.6 bits)
S2: 51 (24.3 bits)

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_198156084.1 AKL27_RS25140 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_001189915.1:WP_198156084.1
          Length = 216

 Score =  367 bits (943), Expect = e-106
 Identities = 182/216 (84%), Positives = 200/216 (92%), Gaps = 1/216 (0%)

Query: 341 CLTITGRTLAEELENVPDTPRADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLK 400
           C+TITGRTLAEEL  +PD  RADQDVILPI+KALY +GHLAILKGNLA EG VAKITGLK
Sbjct: 1   CITITGRTLAEELAAIPDL-RADQDVILPIDKALYKQGHLAILKGNLAPEGCVAKITGLK 59

Query: 401 NPVITGPARVFEDEQSAMEAILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGL 460
           NPVITGPARVFEDE +AM+AILAD+I  GD+LV+RYLGPKGGPGMPEMLAPTSA+IGKGL
Sbjct: 60  NPVITGPARVFEDEYTAMDAILADQIKPGDVLVMRYLGPKGGPGMPEMLAPTSALIGKGL 119

Query: 461 GESVGFITDGRFSGGTWGMVVGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEE 520
           GESVG ITDGRFSGGTWGMVVGHVAPEA+VGG IALV+EGDS+TIDAH+ L+QLNVADEE
Sbjct: 120 GESVGLITDGRFSGGTWGMVVGHVAPEAFVGGVIALVKEGDSVTIDAHQQLIQLNVADEE 179

Query: 521 LARRRANWKQPAPRYTRGVLAKFSKLASTASKGAVT 556
           +ARRR  WKQPAPRYTRGVLAK++ LASTASKGAVT
Sbjct: 180 IARRRTEWKQPAPRYTRGVLAKYAALASTASKGAVT 215


Lambda     K      H
   0.316    0.133    0.386 

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: 461
Number of extensions: 20
Number of successful extensions: 2
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: 557
Length of database: 216
Length adjustment: 29
Effective length of query: 528
Effective length of database: 187
Effective search space:    98736
Effective search space used:    98736
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Jul 25 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:

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
the source code
instructions for running GapMind on your computer
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