GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate AO353_03840 AO353_03840 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03840
          Length = 351

 Score =  226 bits (577), Expect = 5e-64
 Identities = 128/335 (38%), Positives = 193/335 (57%), Gaps = 6/335 (1%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           M+ L + N+ KRYG    +K +++ L  G+ +  LG SGCGK+TLL +IAGL   SGG+I
Sbjct: 1   MTGLILENVEKRYGTACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
            + +  +       R+  MVFQS AL+P+++V  NI + L++R V + +    V +   L
Sbjct: 61  RLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELLEL 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           +Q++ ++DR  ++LSGGQRQRVAI RA+  +P++ L DEPLS LDAKLR  M+ E+++L 
Sbjct: 121 IQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
           Q L  T + VTHDQ EAMT+A  + V+   R++Q+  P E+Y  PA  +VA F+GS   N
Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGQNRVQQVGTPIEIYRHPANEFVADFIGSG--N 238

Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLA--AGSEAQRLTA 298
           I  A    +G       + L +P     +   G +VK+ +RPE L+L+    +   RL  
Sbjct: 239 IFPATALGDGKVGLPGGDALQVPIC--SSIVVGEKVKMLVRPEDLQLSHPQATAGNRLLG 296

Query: 299 SVEVVELTGPELVTTATVGSQRITACLPPRTAVGM 333
            V  V   G  + TT       +TA   P   +G+
Sbjct: 297 RVTFVRDIGATIETTVECSGVTLTALSTPCQGIGL 331


Lambda     K      H
   0.320    0.136    0.385 

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: 297
Number of extensions: 18
Number of successful extensions: 2
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: 360
Length of database: 351
Length adjustment: 29
Effective length of query: 331
Effective length of database: 322
Effective search space:   106582
Effective search space used:   106582
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 (21.8 bits)
S2: 49 (23.5 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