GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Pf6N2E2_3128 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3128
          Length = 345

 Score =  169 bits (427), Expect = 1e-46
 Identities = 96/233 (41%), Positives = 139/233 (59%), Gaps = 6/233 (2%)

Query: 37  QVLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDI 96
           QV  + G V  V+ + + I  GE F ++G SGSGK+T +R       P++G+I + GE+ 
Sbjct: 9   QVSRQFGDVKAVDRVCIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIHGEEA 68

Query: 97  LQLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTV 156
                  L  ++R  ++ VFQ + L PH +V DNVAYGLKV+G +K    +RA   +  V
Sbjct: 69  T-----GLAPYQRD-VNTVFQDYALFPHMNVRDNVAYGLKVKGVAKAERIKRADEALEMV 122

Query: 157 GLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQK 216
            L GY  + P QLSGG RQRV LARAL     ++L+DE   ALD  +R +MQ +L +LQ+
Sbjct: 123 ALGGYGERKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQR 182

Query: 217 TLHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269
            L  T +F+THD  EA+ + +R+A+   G++ QV TPR +   PA  +V  FV
Sbjct: 183 QLGITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATTFVAEFV 235


Lambda     K      H
   0.321    0.138    0.387 

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: 216
Number of extensions: 8
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: 276
Length of database: 345
Length adjustment: 27
Effective length of query: 249
Effective length of database: 318
Effective search space:    79182
Effective search space used:    79182
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: 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