GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Pseudomonas fluorescens FW300-N2E2

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Pf6N2E2_3426 Peptide ABC transporter, ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3426
          Length = 323

 Score =  254 bits (649), Expect = 2e-72
 Identities = 137/294 (46%), Positives = 194/294 (65%), Gaps = 4/294 (1%)

Query: 30  LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEM 89
           +KAV+G+S+ +  GE LGLVGESG GKSTLGR IL+L     G+I F+G D+      ++
Sbjct: 28  VKAVNGVSLSLAPGEVLGLVGESGSGKSTLGRAILRLTEVSAGQILFDGVDMAQGKRIDI 87

Query: 90  KPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGREF 149
           +  R +  +IFQDP  +LNP+M++G  + + L +         R+RV+ELL++VG+  E 
Sbjct: 88  ERLRHETAMIFQDPYTALNPRMSIGDTLAEVLRVRCAIPASLIRQRVDELLNLVGLRPEL 147

Query: 150 INSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGIS 209
            +  P   SGGQ QR+GIARALA+ P+ I+ DE V+ALDVSIQ QII+LL E++Q+M ++
Sbjct: 148 ADRKPGSLSGGQCQRVGIARALAIEPRLIIADECVAALDVSIQGQIINLLLELRQRMNLA 207

Query: 210 YLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQK 269
            LFIAH+LA+V  +  +VAVMYLG+IVE G  + +F NP HPYT AL++S+P I  D  +
Sbjct: 208 ILFIAHDLAIVRRLCDRVAVMYLGEIVEQGPTEAVFSNPRHPYTVALIQSIPHI--DPTR 265

Query: 270 QRFYS-LKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHL 322
               + L GE PSP++LP GC F  RC   + IC +  P + ++   H  SC L
Sbjct: 266 PLLSAPLPGEPPSPLNLPSGCAFHPRCRYAQPICAKTPPPIHDI-NGHRYSCVL 318


Lambda     K      H
   0.321    0.142    0.417 

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: 10
Number of successful extensions: 3
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: 328
Length of database: 323
Length adjustment: 28
Effective length of query: 300
Effective length of database: 295
Effective search space:    88500
Effective search space used:    88500
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: 48 (23.1 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