Aligments for a candidate for mtlE in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for mtlE in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, periplasmic substrate-binding protein (characterized)
to candidate AO356_27670 AO356_27670 sugar ABC transporter substrate-binding protein

Query= reanno::WCS417:GFF2493
         (440 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27670
          Length = 436

 Score =  842 bits (2174), Expect = 0.0
 Identities = 413/440 (93%), Positives = 426/440 (96%), Gaps = 4/440 (0%)

Query: 1   MKFTAKALLASTCMMTCMTLSAVSFGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLN 60
           MK + KALL STCM    TLS+VSFGAQTLTIATVNNSDMIRMQKLSKTFEAEHP+IKLN
Sbjct: 1   MKPSVKALLVSTCM----TLSSVSFGAQTLTIATVNNSDMIRMQKLSKTFEAEHPDIKLN 56

Query: 61  WVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFP 120
           WVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFP
Sbjct: 57  WVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFP 116

Query: 121 SVRDGLSVKGSLYALPFYAESSITYYRTDLFKDAGLTMPEHPTWTQIGEFASKLTDKTKE 180
           SVRDGLSVKGSLYALPFYAESSITYYRTDLFK+AGLTMPEHPTWTQIGEFA KLTDK+KE
Sbjct: 117 SVRDGLSVKGSLYALPFYAESSITYYRTDLFKNAGLTMPEHPTWTQIGEFAEKLTDKSKE 176

Query: 181 QYGLCLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGP 240
           QYGLCLRGKAGWGENMALITTLANGYGARWFDEKWQP+FNGPEWKDALNFYVDNMKKSGP
Sbjct: 177 QYGLCLRGKAGWGENMALITTLANGYGARWFDEKWQPQFNGPEWKDALNFYVDNMKKSGP 236

Query: 241 PGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTS 300
           PGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKV+DHVGFTFAPHEKTDKGTS
Sbjct: 237 PGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVSDHVGFTFAPHEKTDKGTS 296

Query: 301 WLYSWSLAIPTSSKAKDAAKVFTSWATSKEYGELVAKTDGIANVPPGTRKSTYNDEYMKA 360
           W+YSWSLAIPTSSKAK+AA VFT+WATSKEY +LVAKTDGIANVPPGTR STY+DEYMKA
Sbjct: 297 WMYSWSLAIPTSSKAKEAATVFTTWATSKEYSQLVAKTDGIANVPPGTRTSTYSDEYMKA 356

Query: 361 APFAKVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDA 420
           APFAKVTLESLKVADP  PTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVD 
Sbjct: 357 APFAKVTLESLKVADPKAPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDQ 416

Query: 421 ALTAAQTTTEREMKRAGYPK 440
           ALTAAQ+TTEREMKRAGYPK
Sbjct: 417 ALTAAQSTTEREMKRAGYPK 436


Lambda     K      H
   0.315    0.130    0.394 

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: 821
Number of extensions: 29
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: 440
Length of database: 436
Length adjustment: 32
Effective length of query: 408
Effective length of database: 404
Effective search space:   164832
Effective search space used:   164832
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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 catabolism of small carbon sources