GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TRIC in Shewanella loihica PV-4

Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 5208513 Shew_1024 hypothetical protein (RefSeq)

Query= reanno::ANA3:7023996
         (213 letters)



>FitnessBrowser__PV4:5208513
          Length = 206

 Score =  163 bits (413), Expect = 2e-45
 Identities = 81/193 (41%), Positives = 124/193 (64%), Gaps = 1/193 (0%)

Query: 12  LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLA 71
           L G    A++GALAAGR +MD FGV+++   TAIGGG++RD LLG  P+ W+ + +Y++ 
Sbjct: 10  LCGTAVFALSGALAAGRHRMDPFGVIVLASVTAIGGGSIRDALLGTTPVFWIRDPNYIIV 69

Query: 72  IAFASLLTVAIAPVMRYLSKLFLAI-DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130
           I    LL +      + + +  L + DA GLA+F+++GA+K L LG S  IAVVMGL+TG
Sbjct: 70  ILATVLLALLFIRKPKKVPQYTLPVADAFGLALFTVIGAEKALNLGLSGMIAVVMGLITG 129

Query: 131 VFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGFSLRM 190
           V GG+IRDILC Q+P+I + E+YA  S+F    Y     + LA+ + L + +     +R+
Sbjct: 130 VGGGIIRDILCRQIPMILRTEIYATASIFGGISYTCAITWGLADKVALAIAMISALVIRL 189

Query: 191 LALRYHWSMPTFD 203
            A+++H  +P F+
Sbjct: 190 AAIKWHLRLPAFE 202



 Score = 33.9 bits (76), Expect = 2e-06
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 97  DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIFKKE-LYAV 155
           D  G AVF++ GA         P   +V+  VT + GG IRD L    P+ + ++  Y +
Sbjct: 9   DLCGTAVFALSGALAAGRHRMDPFGVIVLASVTAIGGGSIRDALLGTTPVFWIRDPNYII 68

Query: 156 ISLFT 160
           + L T
Sbjct: 69  VILAT 73


Lambda     K      H
   0.330    0.143    0.438 

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: 141
Number of extensions: 7
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 213
Length of database: 206
Length adjustment: 21
Effective length of query: 192
Effective length of database: 185
Effective search space:    35520
Effective search space used:    35520
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: 45 (21.9 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 (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