GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treEIIA in Pseudomonas simiae WCS417

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::P39816
         (631 letters)



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

 Score =  440 bits (1132), Expect = e-128
 Identities = 234/501 (46%), Positives = 325/501 (64%), Gaps = 21/501 (4%)

Query: 1   MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAV 60
           M++   + LQ+LGRALM P+A+LP AGLLLR GD DLLNI ++ DAG  +F NL LIFA+
Sbjct: 1   MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAVMHDAGQAIFANLALIFAI 60

Query: 61  GVAIGLA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIG 119
           G+A+G A    G AGLA  IGYL++  TL  M             +  I+MG+  GI  G
Sbjct: 61  GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVM-------------DTSINMGMLAGIASG 107

Query: 120 LLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSL 179
           L+A  LY RF  I+L   L FF G+RFVPI+T  S++ +GVIF  +WP IQ+GIN+   L
Sbjct: 108 LMAGGLYNRFKDIKLPEYLAFFGGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGINSFGVL 167

Query: 180 IADS-TVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238
           + +S ++G F +    RLLI  GLHHI     +F+ G +TDP TG  VTGDLTR+FAGDP
Sbjct: 168 LMESGSLGAFVFGVFNRLLIVTGLHHILNNMAWFVFGSFTDPVTGAVVTGDLTRYFAGDP 227

Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298
             G+FM G FP M+F LPA  LA+   A PE++K++ G+ +S ALTS LTG+TEP+EF+F
Sbjct: 228 KGGQFMTGMFPVMLFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAF 287

Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVF 358
           +F+AP LYLI+++L G+   V ++ ++  G+TFSGG ID VL +G STNGW+V PVG+ +
Sbjct: 288 MFLAPFLYLIHAVLTGLSMAVTNMLNIHLGFTFSGGFIDMVLGWGKSTNGWLVFPVGLAY 347

Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418
           A IYY +F + I  +NLKTPGR   ED Q  +   ++ +Q A   +QALGG QN+ ++ A
Sbjct: 348 ALIYYSVFNYCIRHFNLKTPGR---EDTQVVQAEAMSDNQRATAYIQALGGAQNLLSVGA 404

Query: 419 CITRLRVTVHQPSQVCKDELKRLGAVGVLEVNN--NFQAIFGTKSDALKDDIKTIMAGGV 476
           C TRLR+ +   ++    ELK LGA+ V+   N  + Q + G  +D++ D+I+  M G V
Sbjct: 405 CTTRLRLDMVDRNKAVDAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAMPGFV 464

Query: 477 PATAAALDTVTDKPLKPDSDE 497
            A    +  V +KP+  +  E
Sbjct: 465 AAAPVVVAPV-EKPVAVNVQE 484



 Score = 37.4 bits (85), Expect = 2e-06
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 390 EKAPVAKDQLAFHVLQALGGQQNIANLDA-CITRLRVTVHQPSQVCKDELKRLGAVGVLE 448
           EK      Q A   L ALGG+ N+  L+A  +TRLRV +   S + + +L  LG  GV +
Sbjct: 475 EKPVAVNVQEAEKWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQ 534

Query: 449 VNNN-FQAIFGTKSDALKDDIKTIM 472
           + +  +  + G K+  L + ++ ++
Sbjct: 535 LESGVWHLLIGDKATGLGEALERLV 559


Lambda     K      H
   0.324    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: 905
Number of extensions: 49
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 631
Length of database: 568
Length adjustment: 37
Effective length of query: 594
Effective length of database: 531
Effective search space:   315414
Effective search space used:   315414
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: 41 (22.0 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:

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:

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:

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