GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Pseudomonas fluorescens FW300-N1B4

Align Inositol transport system ATP-binding protein (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          Length = 526

 Score =  169 bits (429), Expect = 8e-47
 Identities = 88/247 (35%), Positives = 150/247 (60%), Gaps = 5/247 (2%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66
           L+ +  + K F  V+AL+ V + V PG    L+G+NGAGKST +K ++G+++P  G++  
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 67  EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126
            G+P+ F  P  A+ AGIA +HQ L ++P MS++ N ++G E   ++  L + DH   +R
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE---QLNGLHMIDHREMHR 148

Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186
            T + + ++ INL  P++ VG LS  ERQ V IA+AV + + +LI+DEPTSA+  ++ A+
Sbjct: 149 CTAKLLERLRINL-DPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAH 207

Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246
           + + I  +++QG  +++ITH +    ++ D   V   G  +G  +   +  + L  MM  
Sbjct: 208 LFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMV- 266

Query: 247 GQELATL 253
           G+EL+ L
Sbjct: 267 GRELSQL 273



 Score = 97.4 bits (241), Expect = 5e-25
 Identities = 64/225 (28%), Positives = 110/225 (48%), Gaps = 7/225 (3%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85
           VS D+  GE   + G  G+G++   + + G+     G+I  +G+ +  +DP  AI  G A
Sbjct: 300 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFA 359

Query: 86  TVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEM-RKMGINLRG 141
            + +      + P +SV  N  M   P   +G    F    A R   E+M +K+ +    
Sbjct: 360 LLTEDRKLSGLFPCLSVLENMEMAVLP-HYVG--NGFIQQKALRALCEDMCKKLRVKTPS 416

Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201
            +Q + TLSGG +Q   +AR +    ++LILDEPT  + V   A +   I  +  +G+AV
Sbjct: 417 LEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAV 476

Query: 202 VFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246
           + I+  +   L + DR  V++ G  +GT  R + + E +  + +G
Sbjct: 477 IMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 521


Lambda     K      H
   0.321    0.137    0.395 

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: 307
Number of extensions: 22
Number of successful extensions: 4
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: 261
Length of database: 526
Length adjustment: 30
Effective length of query: 231
Effective length of database: 496
Effective search space:   114576
Effective search space used:   114576
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: 49 (23.5 bits)

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

Links

Downloads

Related tools

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