Alignments for a candidate for glyXL in Caldicellulosiruptor kronotskyensis 2002

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyXL in Caldicellulosiruptor kronotskyensis 2002

Align UPF0210 protein BL1209 (characterized, see rationale)
to candidate WP_013429568.1 CALKRO_RS02620 PFL family protein

Query= uniprot:Q8G510
         (454 letters)



>NCBI__GCF_000166775.1:WP_013429568.1
          Length = 452

 Score =  510 bits (1313), Expect = e-149
 Identities = 258/454 (56%), Positives = 333/454 (73%), Gaps = 2/454 (0%)

Query: 1   MLNIMEVHETNQMIEQEKLDVRTITMGISLLDCASDDVDKTCDNIYRKITTYAKDLVSTG 60
           M    E+ ET  M++Q  LD+RTIT+GI+L DC+SD   +  DN+ +KI  YA +L +  
Sbjct: 1   MFTSQEIIETINMVKQSNLDIRTITVGINLFDCSSDIPQRFIDNMRKKIIKYAGNLKNVA 60

Query: 61  KAIERDYGIPIVNKRITVTPISLVGASSCKTSEDFVKIAHALDKAAKEVGVDLIGGYSAL 120
             IE  +G+PIVN+R+ +TPISL+  S   + ED +++A A+D+ AKE+ VDLIGGYSA 
Sbjct: 61  NEIEDMFGLPIVNRRVALTPISLLTFSY--SYEDLIEVALAIDEIAKELEVDLIGGYSAA 118

Query: 121 VSKSMTPAEELLIRSLPQALSETDIVCSSVNVGSTKTGIDMNAVELLGHIIKDVAERTAD 180
           V KS     +  I S+P AL+ TD +CSSV+VG+T+ GI+++ +  LG IIKD+A++T D
Sbjct: 119 VHKSYDENTKKFISSIPDALASTDRLCSSVDVGTTRAGINLDVIAHLGFIIKDIAQKTKD 178

Query: 181 NDSYGCVKFVAFCNVPDDNPFMAGGFHGVTEGDAVINVGVSGPGVVSRALDAAKGKDFEF 240
            DS+GC +FV F N PDDNPFMAG FHG  EGD+ INVG+SGPGVV RAL+  K    + 
Sbjct: 179 KDSFGCARFVVFANAPDDNPFMAGAFHGTGEGDSAINVGISGPGVVKRALEEKKYASIDE 238

Query: 241 LCETIKRTAFKITRVGQLVAQEASRRLGIPFGIIDLSLAPTPAVGDSVGEVLEKIGLEQV 300
           + ETIK+ AFKITR GQLV Q AS++L IP GI+DLSLAPTP VGDS+ E+LE+IGLE+V
Sbjct: 239 IYETIKKMAFKITRAGQLVLQYASKKLQIPAGIVDLSLAPTPKVGDSIAEILEEIGLEKV 298

Query: 301 GAPGTTAALAMLNDQVKKGGIMASSYVGGLSGAFIPVSEDKNMIDAASSDCLTIEKLEAM 360
           G  GTT ALA+LND VKKGG MA+++ GGLSGAFIPVSED  M+ A  +  L++EKLEAM
Sbjct: 299 GGYGTTFALALLNDAVKKGGAMAATFTGGLSGAFIPVSEDSGMVRAVEAGTLSLEKLEAM 358

Query: 361 TCVCSVGLDMIAIPGDTSASTISGLIADEAAIGMVNQKTTAVRVIPVAGKGVGEMANFGG 420
           T VCSVGLDMI +PGD  A  IS +IADE AIG+ N KTTAVRVIP  GK  G+  NFGG
Sbjct: 359 TSVCSVGLDMIVVPGDVEAEVISAMIADEIAIGVYNNKTTAVRVIPAYGKKEGDEVNFGG 418

Query: 421 LMGYAPIMPVNQTSCEAFVTRGGRIPAPIHSFKN 454
           L+G + +M VN++S +  + RGGR+P PI S +N
Sbjct: 419 LLGRSKVMSVNRSSPKRLIERGGRVPPPIISLRN 452


Lambda     K      H
   0.317    0.134    0.380 

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: 614
Number of extensions: 25
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: 454
Length of database: 452
Length adjustment: 33
Effective length of query: 421
Effective length of database: 419
Effective search space:   176399
Effective search space used:   176399
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: 51 (24.3 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:

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 2024 update 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 original 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