Alignments for a candidate for ams in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ams in Klebsiella michiganensis M5al

Align β-fructohydrolase (ScrB) (intracellular) (EC 3.2.1.26) (characterized)
to candidate BWI76_RS07310 BWI76_RS07310 sucrose-6-phosphate hydrolase

Query= CAZy::AAS47898.1
         (466 letters)



>FitnessBrowser__Koxy:BWI76_RS07310
          Length = 466

 Score =  870 bits (2249), Expect = 0.0
 Identities = 407/466 (87%), Positives = 422/466 (90%)

Query: 1   MSLPSRLPAILQAVMQGQPRALADSHYPRWHHAPVTGLMNDPNGFIEFAGRYHLFYQWNP 60
           MSLPSRLPAILQAVMQGQPRALADSHYPRWHHAPVTGLMNDPNGF+EFAGRYHLFYQWNP
Sbjct: 1   MSLPSRLPAILQAVMQGQPRALADSHYPRWHHAPVTGLMNDPNGFVEFAGRYHLFYQWNP 60

Query: 61  LACDHTFKCWAHWSSIDLLHWQHEPIALMPDEEYDRNGCYSGSAVDNNGTLTLCYTGNVK 120
           LACDH FKCWAHWSS DLL W+HEPIALMPDEEYDRNGCYSGSAVDNNGTLTLCYTGNVK
Sbjct: 61  LACDHKFKCWAHWSSDDLLRWRHEPIALMPDEEYDRNGCYSGSAVDNNGTLTLCYTGNVK 120

Query: 121 FAEGGRTAWQCLATENADGTFRKIGPVLPLPEGYTGHVRDPKVWRHEDLWYMVLGAQDRQ 180
           F +GGRTAWQCLATENADGTF K+GPVLPLPEGYTGHVRDPKVWRH+D WYMVLGAQDRQ
Sbjct: 121 FDDGGRTAWQCLATENADGTFTKLGPVLPLPEGYTGHVRDPKVWRHQDRWYMVLGAQDRQ 180

Query: 181 KRGKVLLFSSADLHQWTSMGEIAGHGINGLDDVGYMWECPDLFPLGDQHILICCPQGIAR 240
           KRGKVLLFSS DLHQW S GEIAG GINGL D GYMWECPDLF LGDQHILICCPQGIAR
Sbjct: 181 KRGKVLLFSSPDLHQWRSEGEIAGDGINGLSDAGYMWECPDLFALGDQHILICCPQGIAR 240

Query: 241 EEECYLNTYPAVWMAGEFDYAAGAFRHGELHELDAGFEFYAPQTMLTSDGRRLLVGWMGV 300
           EEE +LNTYPAVWMAG FDY   AF HGEL ELDAGFEFYAPQT  T DGRRLLVGWMGV
Sbjct: 241 EEERFLNTYPAVWMAGGFDYDRAAFSHGELRELDAGFEFYAPQTTHTRDGRRLLVGWMGV 300

Query: 301 PEGEEMLQPTLNNGWIHQMTCLRELEFINGQLYQRPLRELSALRGEANGWSGNALPLAPM 360
           P+GEEM QPTL +GWIHQMTCLRELEFI+GQLYQRPLREL+ALRGEA+GW GNALPLAPM
Sbjct: 301 PDGEEMRQPTLAHGWIHQMTCLRELEFIDGQLYQRPLRELTALRGEAHGWQGNALPLAPM 360

Query: 361 EIDLQTRGGDMLSLDFGGVLTLECDASGLRLARRSLASDEMHYRYWRGNVRSLRVFIDQS 420
           EI LQT   D LSLDFGG LTLE DASG+RLARRSL SDEMHYRYWRG VR+LR+F D+S
Sbjct: 361 EIALQTAADDALSLDFGGALTLERDASGIRLARRSLVSDEMHYRYWRGEVRTLRIFFDRS 420

Query: 421 SVEIFINGGEGVMSSRYFPACSGQLTFSGITPDAFCYWPLRTCMVE 466
           SVEIFIN GEGVMSSR FPA   QL FSG  PDAFCYWPLRTCMVE
Sbjct: 421 SVEIFINDGEGVMSSRCFPAYPAQLIFSGSAPDAFCYWPLRTCMVE 466


Lambda     K      H
   0.322    0.139    0.468 

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: 1060
Number of extensions: 46
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: 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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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)
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

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