GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Dechlorosoma suillum PS

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__PS:Dsui_0629
          Length = 307

 Score =  143 bits (361), Expect = 4e-39
 Identities = 91/301 (30%), Positives = 164/301 (54%), Gaps = 21/301 (6%)

Query: 1   MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVN 60
           MDI  +Q I+NG+ +GSI AL A+G T+ YGIL L NFAHG+ + +GA     V      
Sbjct: 1   MDI-FLQQIINGLVLGSIYALVALGYTMVYGILGLINFAHGEVVMIGALTALTVVKLLAG 59

Query: 61  IWL-SMIVAVVGTVGVMLLS-------EKLLWSRMRSIRANSTTLIIISIGLALFLRNGI 112
             L   ++A++G +    +        EK+ +  +R  +A     +I +IG+++ L+N  
Sbjct: 60  SGLPGPVIALIGLMAAAPVCMAIGYGIEKIAYRPLR--KAPRLAPLITAIGVSIVLQNLA 117

Query: 113 ILIWGGRNQNYNLPI-TPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRA 171
           +++WG    ++   +   A ++ G      Q++++ +A   +  L  L+  T++G+AMRA
Sbjct: 118 MMVWGRSYHSFPAVLPAEAHEVLGATFTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMRA 177

Query: 172 VADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILPLFASV 230
            A++  +A++ G++V  +I  T++I   + ++ G M     +     MG+ L L  F + 
Sbjct: 178 TAENPAIAQLMGVNVNHIISLTFVIGSALAAVAGLMVSANYSIAHYYMGFILGLKAFTAA 237

Query: 231 ILGGIGNPYGAIAAAFIIGIVQ--------EVSTPFLGSQYKQGVALLIMILVLLIRPKG 282
           +LGGIGN  GA+    ++G+++        +++  FLGS Y+   A  ++ILVL+ RP G
Sbjct: 238 VLGGIGNLAGAMIGGILLGLIESLGAGYIGDITGGFLGSHYQDVFAFFVLILVLVFRPSG 297

Query: 283 L 283
           L
Sbjct: 298 L 298


Lambda     K      H
   0.328    0.144    0.426 

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: 233
Number of extensions: 17
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: 288
Length of database: 307
Length adjustment: 26
Effective length of query: 262
Effective length of database: 281
Effective search space:    73622
Effective search space used:    73622
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 (21.7 bits)
S2: 48 (23.1 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