GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas fluorescens FW300-N2C3

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AO356_29015 AO356_29015 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29015
          Length = 293

 Score =  124 bits (310), Expect = 3e-33
 Identities = 91/306 (29%), Positives = 156/306 (50%), Gaps = 19/306 (6%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAAL-IVFLVLTS 59
           M +F++ L+ GL  G++Y LVAIG+ ++Y   G+ NFA G + +   FAAL  V L    
Sbjct: 1   MNFFLETLIGGLLAGTLYSLVAIGFVLIYKASGVFNFAQGAMLL---FAALTFVSLREQG 57

Query: 60  IFAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFI 119
           +   L + + +LVM+V A+L        IER+  RPL    ++   +  +G+S  +    
Sbjct: 58  LSFALALLLTVLVMVVGALL--------IERLVLRPLVNRSQITLFMATLGLSFIIEGLA 109

Query: 120 QVTQGPRNKPIPPMVSSVYQF-GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178
           Q   G + + +   +  V  F G I +S   +I   ++A+ + +   + N+T +G A RA
Sbjct: 110 QGLMGAQVRALDLGIEDVPLFVGEIMISQFDLIAAGVSALTVAVLALLFNKTRIGVALRA 169

Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238
              D + A  LG+N+++   I + +   +  VAG ++    GV  F+      +KA    
Sbjct: 170 VADDTRAALSLGINLNRIWQIVWAVAGVVGLVAGLLWGARQGV-QFSLSLVV-LKALPVL 227

Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYF--TIAYKDVATFA-ILAFVLIF-KPTGILGR 294
           ++GG  S+ GA+ GGL++G  E+L  AY    I       FA  LA + ++ +P G+ G 
Sbjct: 228 IIGGFTSIGGAIVGGLIVGAAENLAEAYIGPLIGGGITPWFAYFLALIFLYIRPAGLFGD 287

Query: 295 PEVEKV 300
             +E+V
Sbjct: 288 RIIERV 293


Lambda     K      H
   0.329    0.143    0.421 

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: 293
Number of extensions: 26
Number of successful extensions: 5
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: 300
Length of database: 293
Length adjustment: 26
Effective length of query: 274
Effective length of database: 267
Effective search space:    73158
Effective search space used:    73158
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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