Aligments for a candidate for nagEcb in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagEcb in Pseudomonas simiae WCS417

Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter

Query= reanno::pseudo3_N2E3:AO353_04465
         (571 letters)



>lcl|FitnessBrowser__WCS417:GFF4494 PS417_23000 PTS
           N-acetyl-D-glucosamine transporter
          Length = 568

 Score =  928 bits (2398), Expect = 0.0
 Identities = 466/569 (81%), Positives = 502/569 (88%), Gaps = 3/569 (0%)

Query: 1   MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60
           MYQ FIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIA++HDAGQ IFANLALIFAI
Sbjct: 1   MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAVMHDAGQAIFANLALIFAI 60

Query: 61  GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI 120
           GIAVGFARDNNGTAGLAGAIGYLVMVSTLKV+D SINMGMLAGI SGLMAG LYNRFKDI
Sbjct: 61  GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVMDTSINMGMLAGIASGLMAGGLYNRFKDI 120

Query: 121 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG 180
           KLPEYLAFFGGRRFVPI TGFSAVGLGVIFGLIWPPIQHGINSFG LL+ESGS+GAFVFG
Sbjct: 121 KLPEYLAFFGGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGINSFGVLLMESGSLGAFVFG 180

Query: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240
           VFNRLLIVTGLHHILNNMAWF+FGSFTDP TGA+VTGDL RYFAGDPKGGQFMTGMFP+M
Sbjct: 181 VFNRLLIVTGLHHILNNMAWFVFGSFTDPVTGAVVTGDLTRYFAGDPKGGQFMTGMFPVM 240

Query: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300
           +FGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAP LYL+H +
Sbjct: 241 LFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAV 300

Query: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360
           LTG++MA+TN LNIHLGFTFSGG IDM LGWGKSTNGWLVFPVGLAYA+IYY VF++CIR
Sbjct: 301 LTGLSMAVTNMLNIHLGFTFSGGFIDMVLGWGKSTNGWLVFPVGLAYALIYYSVFNYCIR 360

Query: 361 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS 420
            FNLKTPGRE   V +   +S+NQRA AYIQALGGA+NL++VGACTTRLRL+MVDRNKA 
Sbjct: 361 HFNLKTPGREDTQVVQAEAMSDNQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKAV 420

Query: 421 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA 480
           D+ELKALGAMAVVRPG GGSLQVVVGP+ADSIADEIR AMP     + AA VV     K 
Sbjct: 421 DAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAMP---GFVAAAPVVVAPVEKP 477

Query: 481 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG 540
             V   EA+KWLNA+GG  NV QL+ VAMTR+R++L D   LSE  L  LGCQGVS L+ 
Sbjct: 478 VAVNVQEAEKWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLES 537

Query: 541 GVWHLLIGDKALSLSEALEGLVNRSEVSA 569
           GVWHLLIGDKA  L EALE LV   ++ A
Sbjct: 538 GVWHLLIGDKATGLGEALERLVGAQQIGA 566


Lambda     K      H
   0.325    0.142    0.421 

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: 1130
Number of extensions: 55
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: 571
Length of database: 568
Length adjustment: 36
Effective length of query: 535
Effective length of database: 532
Effective search space:   284620
Effective search space used:   284620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

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

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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