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

GapMind for Amino acid biosynthesis

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

Align Anthranilate synthase component I (characterized, see rationale)
to candidate WP_066328935.1 BLR17_RS13350 anthranilate synthase component I family protein

Query= uniprot:A0A1X9ZB07_9SPHI
         (466 letters)



>NCBI__GCF_900100165.1:WP_066328935.1
          Length = 466

 Score =  524 bits (1349), Expect = e-153
 Identities = 259/467 (55%), Positives = 352/467 (75%), Gaps = 7/467 (1%)

Query: 3   YKINTTYKKMLADTTTPVSIYLRLRDVYPNSILLESSDYHSRENSMSFVCADPVAGIILK 62
           +K+NT +K++LADT TPVS+Y ++RD +PNS+LLESSDYH+ +NS S++C +P+A I ++
Sbjct: 4   FKLNTKFKQILADTITPVSVYFKIRDKFPNSLLLESSDYHANDNSFSYICCNPIASIKIE 63

Query: 63  GSRLETYFPDGAVEITE---SKNLIEEITDFKDKFSETELPEIKFISSGLFGYFTWNAVQ 119
              +   FPDG+ E T      N+ E I  F  +F ++E    KFI++GLFGY +++AV+
Sbjct: 64  NETIFKQFPDGSSETTTIDAKTNIPEVIQQFSGQF-KSEKNNFKFINNGLFGYISYDAVR 122

Query: 120 HFEDIKFTSETPEGEEIPEMQYHLYRYIIAIDHFKNEITLFKNTFEGEEEGGLEKMEYLI 179
           +FE +    +      IP++ Y +Y+ IIAI+HFKNE  +F ++ +  ++  + ++E L+
Sbjct: 123 YFEKVTIAKKE-NSNTIPDLFYAVYQNIIAINHFKNEAYIFCHSVD--DKNNIAEIEQLM 179

Query: 180 QNKNYPEYKFQLRGEESSNLTDQGFMDLVEKLQKHIYRGDVFQIVPSRAFKQAFSGDEFN 239
           Q++N P YKF   GE  SNLTD+ F   V   +KH +RGDVFQ+V SR F Q F GDEFN
Sbjct: 180 QSRNIPSYKFSKEGEGFSNLTDEEFKHNVALAKKHCFRGDVFQLVLSRRFTQGFKGDEFN 239

Query: 240 VYRCLRSINPSPYLFYFDYGNFKLFGSSPEAQITIKNNSANIFPIAGTFKRSGNDIEDAE 299
           VYR LRSINPSPYLF+FDYG+FK+FGSSPEAQI +K+  A I PIAGTF+R+G+D +DA 
Sbjct: 240 VYRALRSINPSPYLFFFDYGDFKIFGSSPEAQIIVKDRKAEIHPIAGTFRRTGDDEKDAV 299

Query: 300 QARKLEQDPKESAEHVMLVDLARNDLSRHCNRVEVKSFKEVQYYSHLIHLVSKVSGHLQE 359
            A+KL +D KE++EHVMLVDLARNDLSRH + V V+ ++EVQ++SH+IHLVSKV+GHL +
Sbjct: 300 LAKKLSEDKKENSEHVMLVDLARNDLSRHGHNVNVERYREVQFFSHVIHLVSKVTGHLHD 359

Query: 360 NVSAFKVVADTYPAGTLSGAPKYKAMQLIDENEKLGRNFYAGAIGFMGFNEDFNHAIMIR 419
           + +  +VVADT+PAGTLSGAPK++AMQLI++ EK  RNFY GAIGFM F  +FNHAIMIR
Sbjct: 360 DATTMQVVADTFPAGTLSGAPKHRAMQLIEDYEKTNRNFYGGAIGFMDFEGNFNHAIMIR 419

Query: 420 TFMSKNNELHYRAGAGIVADSVPETEMQEVNNKIAALRKAVQMAEGI 466
           TF+SKN++LH +AGAGIVA S  E+EMQEV NK+ AL  A+ +AE I
Sbjct: 420 TFLSKNHQLHSQAGAGIVASSDEESEMQEVYNKLRALNAALDLAETI 466


Lambda     K      H
   0.318    0.135    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: 764
Number of extensions: 37
Number of successful extensions: 4
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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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Protein sequences (fasta format)
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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