Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::P39816
         (631 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17535
          Length = 571

 Score =  434 bits (1117), Expect = e-126
 Identities = 228/485 (47%), Positives = 321/485 (66%), Gaps = 21/485 (4%)

Query: 1   MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAV 60
           M++   + LQ+LGRALM P+A+LP AGLLLR GD DLL+I II DAG  +F NL +IFA+
Sbjct: 1   MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLDIAIIHDAGQAIFANLAMIFAI 60

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

Query: 120 LLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSL 179
           LLA  LY RF  I+L   L FF G+RFVPI+T  S++ +GV+F  +WP IQ GIN   +L
Sbjct: 108 LLAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFSAVGLGVVFGLIWPPIQQGINGFGAL 167

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

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

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

Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418
           A IYY +F F I +++LKTPGRE    G   +K  +A++Q A   +QALGG  N+  + A
Sbjct: 348 AAIYYLVFDFCIRRFDLKTPGREEVPAG---DKPAIAENQRAAAYIQALGGADNLITIGA 404

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

Query: 477 -PATA 480
            P TA
Sbjct: 465 RPVTA 469



 Score = 32.7 bits (73), Expect = 4e-05
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 404 LQALGGQQNIANLDACIT-RLRVTVHQPSQVCKDELKRLGAVGVLEVNNN-FQAIFGTKS 461
           L ALGGQ N+  L+   T RLRV +     + +  LK LG  G+  + +  +  + G K+
Sbjct: 492 LDALGGQDNVLQLECVATSRLRVRLADDKGLSESRLKGLGCQGMSSLEDGVWHLLLGEKA 551

Query: 462 DAL 464
             L
Sbjct: 552 PRL 554


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: 922
Number of extensions: 56
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: 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:

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