GapMind for catabolism of small carbon sources

 

Aligments for a candidate for potA in Pseudomonas fluorescens FW300-N1B4

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Pf1N1B4_2261 Putrescine transport ATP-binding protein PotG (TC 3.A.1.11.2)

Query= TCDB::P31134
         (377 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2261 Putrescine transport
           ATP-binding protein PotG (TC 3.A.1.11.2)
          Length = 380

 Score =  419 bits (1076), Expect = e-122
 Identities = 225/358 (62%), Positives = 272/358 (75%), Gaps = 2/358 (0%)

Query: 19  LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78
           L++I  +TK +D   AVDDVSL I KGEIFALLG SG GKSTLLRMLAGFE+P+ G+I L
Sbjct: 22  LVKIDRVTKKFDETIAVDDVSLEIKKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYL 81

Query: 79  DGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVH 138
           DGVD++ +PPY RPINMMFQSYALFPHMTV QNIAFGLKQDKLP AE+ +RV +ML LV 
Sbjct: 82  DGVDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKLPAAEVDARVADMLKLVQ 141

Query: 139 MQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILER 198
           M ++AKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLR +MQLE+V+I+ER
Sbjct: 142 MSQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIER 201

Query: 199 VGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEG 258
           VGVTCVMVTHDQEEAMTMA RIAIM+ G   QIG P +IYE PT+R   EFIG+VN+F+G
Sbjct: 202 VGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPIDIYETPTSRLVCEFIGNVNIFDG 261

Query: 259 VLKERQEDGLVLDSPGLVHPLKVDADASV-VDNVPVHVALRPEKIMLCEEPPANGCNFAV 317
            + +  E   ++    L   + V    S  V +  V  A+RPEK+++    P    N++ 
Sbjct: 262 EVIDDAEGHAIITCKDLDRQIYVGHGISTSVQDKSVTYAIRPEKLLVTPTMPTCEYNWSS 321

Query: 318 GEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVL 375
           G+V  IAYLG  SV++V L SG+++ + + NA R R   PTWGD+V + WE DS VVL
Sbjct: 322 GKVHDIAYLGGHSVFYVELPSGKIVQSFVANAER-RGQRPTWGDQVYVYWEDDSGVVL 378


Lambda     K      H
   0.321    0.137    0.400 

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: 440
Number of extensions: 9
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: 377
Length of database: 380
Length adjustment: 30
Effective length of query: 347
Effective length of database: 350
Effective search space:   121450
Effective search space used:   121450
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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