GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEIIA in Pseudomonas fluorescens FW300-N2E3

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::P39816
         (631 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04465
          Length = 571

 Score =  438 bits (1126), Expect = e-127
 Identities = 233/494 (47%), Positives = 320/494 (64%), Gaps = 20/494 (4%)

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

Query: 61  GVAIGLA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIG 119
           G+A+G A    G AGLA  IGYL++  TL    K+L            I+MG+  GII G
Sbjct: 61  GIAVGFARDNNGTAGLAGAIGYLVMVSTL----KVLDAS---------INMGMLAGIISG 107

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

Query: 180 IADS-TVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238
           + +S ++G F +    RLLI  GLHHI     +F+ G +TDP+TG  VTGDL R+FAGDP
Sbjct: 168 LLESGSIGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDP 227

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

Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVF 358
           +F+AP+LYL++ +L G+   + +  ++  G+TFSGG ID  L +G STNGW+V PVG+ +
Sbjct: 288 MFLAPLLYLLHVLLTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAY 347

Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418
           A IYY +F F I ++NLKTPGRE    G   EK  ++++Q A   +QALGG +N+  + A
Sbjct: 348 AVIYYVVFDFCIRRFNLKTPGREGVVVG---EKVVLSENQRAGAYIQALGGAENLITVGA 404

Query: 419 CITRLRVTVHQPSQVCKDELKRLGAVGVLE--VNNNFQAIFGTKSDALKDDIKTIMAGGV 476
           C TRLR+ +   ++    ELK LGA+ V+      + Q + G  +D++ D+I+  M    
Sbjct: 405 CTTRLRLEMVDRNKASDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAG 464

Query: 477 PATAAALDTVTDKP 490
            A  AA+    + P
Sbjct: 465 SALVAAVVVTEEAP 478


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: 915
Number of extensions: 50
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: 631
Length of database: 571
Length adjustment: 37
Effective length of query: 594
Effective length of database: 534
Effective search space:   317196
Effective search space used:   317196
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:

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