GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Herbaspirillum seropedicae SmR1

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS21615 HSERO_RS21615 ABC transporter substrate-binding protein

Query= reanno::pseudo3_N2E3:AO353_03055
         (258 letters)



>FitnessBrowser__HerbieS:HSERO_RS21615
          Length = 271

 Score =  116 bits (290), Expect = 6e-31
 Identities = 68/224 (30%), Positives = 115/224 (51%), Gaps = 5/224 (2%)

Query: 28  IGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDAI 87
           +G+E+AY PF+S+     +VGFD DI  AL +++ ++  +V   F+G    L     D +
Sbjct: 51  VGVESAYAPFSSENEQKDVVGFDIDIMKALAKKIGIEVKFVPTPFEGFFNFLAQGDRDLL 110

Query: 88  LSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKKIGVQRGSIHNRFAE 147
           +S+++ITD+RKKSV F+  Y+     + + A       + +LK   +G Q  +  +   +
Sbjct: 111 ISAITITDERKKSVAFSEPYFVATQTIALPAADTKVSKMEDLKPLTVGTQSATSGDELVQ 170

Query: 148 EVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDSGKGFAFVGPAFTD 207
           +VL    A+IK + S      ++ +G +D  VAD  ++ +      + K      P+F  
Sbjct: 171 QVLGKNSAKIKRFDSTPLALKELESGGVDAVVADEPVVKNYIANNPNSKLRTVTDPSFPK 230

Query: 208 EKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQIQDKYF 251
           E Y     GIAVRK D   L KIN  +  ++A+G +  I  +YF
Sbjct: 231 EDY-----GIAVRKDDPELLAKINKGLAEMKADGSFAAISAQYF 269


Lambda     K      H
   0.318    0.138    0.395 

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: 189
Number of extensions: 10
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: 258
Length of database: 271
Length adjustment: 25
Effective length of query: 233
Effective length of database: 246
Effective search space:    57318
Effective search space used:    57318
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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 (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