Alignments for a candidate for aceA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Cupriavidus basilensis 4G11

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate RR42_RS25845 RR42_RS25845 isocitrate lyase

Query= reanno::psRCH2:GFF1971
         (531 letters)



>FitnessBrowser__Cup4G11:RR42_RS25845
          Length = 526

 Score =  881 bits (2276), Expect = 0.0
 Identities = 436/530 (82%), Positives = 475/530 (89%), Gaps = 4/530 (0%)

Query: 1   MSAYQDDIKAVAALKEQYGSSWAAINPESVARMRAQNRFKTGLEIAQYTADIMRKDMAEY 60
           M+ YQDDIKAVA LKE +GS+W AINPE  ARMRAQN+FKTGL+IA+YTA IMR DMA Y
Sbjct: 1   MAQYQDDIKAVAGLKENHGSAWNAINPEYAARMRAQNKFKTGLDIAKYTAKIMRADMAAY 60

Query: 61  DADSSVYTQSLGCWHGFIGQQKLISIKKHLKTTNKRYLYLSGWMVAALRSEFGPLPDQSM 120
           DADSS YTQSLGCWHGFIGQQK+ISIKKH  +T +RYLYLSGWMVAALRSEFGPLPDQSM
Sbjct: 61  DADSSKYTQSLGCWHGFIGQQKMISIKKHFNSTERRYLYLSGWMVAALRSEFGPLPDQSM 120

Query: 121 HEKTAVSDLIEELYTFLRQADSRELDLLFTALDAAREAGDNAKAAEIQNQIDNYETHIVP 180
           HEKT+VS LI ELYTFLRQAD+REL  LF  LDAA+     AKAA IQ +IDN+ TH+VP
Sbjct: 121 HEKTSVSALIRELYTFLRQADARELGGLFRELDAAQGP---AKAA-IQEKIDNHVTHVVP 176

Query: 181 IIADIDAGFGNPEATYLLAKRMIEAGACCIQIENQVSDEKQCGHQDGKVTVPHADFLAKI 240
           IIADIDAGFGN EATYLLAK+ IEAGACCIQIENQVSDEKQCGHQDGKVTVPH DFLAKI
Sbjct: 177 IIADIDAGFGNAEATYLLAKQFIEAGACCIQIENQVSDEKQCGHQDGKVTVPHEDFLAKI 236

Query: 241 AAVRYAFLELGIDNGVIVARTDSLGAGLTKQIAVTKEPGDLGDLYNSFLDCEEVSEAALG 300
            A+RYAFLELG+D+GVIVARTDSLGAGLTKQIAVT   GDLGD YNSFLDCEE+S   LG
Sbjct: 237 RAIRYAFLELGVDDGVIVARTDSLGAGLTKQIAVTNTTGDLGDQYNSFLDCEELSADELG 296

Query: 301 NGDVVIKREGKLLRPKRLPSNLFQFRAGTGEARCILDCITSLQNGADLLWIETEKPHVGQ 360
           NGDV+IKR+GKLLRPKRLPSNLFQFRAGTGEARC+LDC+T+LQNGADLLWIETEKPH+ Q
Sbjct: 297 NGDVIIKRDGKLLRPKRLPSNLFQFRAGTGEARCVLDCVTALQNGADLLWIETEKPHIAQ 356

Query: 361 IAAMVDEIRKTIPNAKLVYNNSPSFNWTLNFRQQVFDAFVAEGKDVSAYDRAKLMSVEYD 420
           I  MV EIRK IPNAKLVYNNSPSFNWTLNFRQQV+DA  A GKDVSAY+R +LM+VEYD
Sbjct: 357 IGGMVSEIRKVIPNAKLVYNNSPSFNWTLNFRQQVYDAMKAAGKDVSAYERTQLMNVEYD 416

Query: 421 ETELAQVADEKIRTFQRDGSAHAGIFHHLITLPTYHTAALSTDNLAKGYFADQGMLAYVK 480
           +TELA++ADEKIRTFQ D S  AGIFHHLITLPTYHTAALSTDNLAK YF DQGML YV 
Sbjct: 417 QTELAKLADEKIRTFQADSSREAGIFHHLITLPTYHTAALSTDNLAKEYFGDQGMLGYVA 476

Query: 481 GVQRQELRQGIACVKHQNMAGSDIGDNHKEYFAGEAALKASGKDNTMNQF 530
           GVQR+E+RQGIACVKHQNM+GSDIGD+HKEYF+GEAALKA+GKDNTMNQF
Sbjct: 477 GVQRKEIRQGIACVKHQNMSGSDIGDDHKEYFSGEAALKAAGKDNTMNQF 526


Lambda     K      H
   0.318    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: 957
Number of extensions: 35
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: 531
Length of database: 526
Length adjustment: 35
Effective length of query: 496
Effective length of database: 491
Effective search space:   243536
Effective search space used:   243536
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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