GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Phyllobacterium brassicacearum STM 196

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_106712951.1 CU102_RS20480 carbohydrate ABC transporter permease

Query= reanno::Koxy:BWI76_RS01820
         (296 letters)



>NCBI__GCF_003010955.1:WP_106712951.1
          Length = 282

 Score =  129 bits (323), Expect = 1e-34
 Identities = 87/278 (31%), Positives = 143/278 (51%), Gaps = 23/278 (8%)

Query: 23  FIAAIMFPLLMVIAISLREGN--FATG-SLIPESISWEHWRLALGFSVEHADGRVTPPPF 79
           ++   +FPL   + IS+   +  ++ G ++ P + +WE++   L         R T  P 
Sbjct: 24  YVIFALFPLFWTLKISVTPQSLLYSEGITMWPSTSTWENYATVL---------RATDFP- 73

Query: 80  PVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVA 139
               +  NS+ V+ ITAI +  ++    YA +R  F GK T+   +L+ Q FP V+ +  
Sbjct: 74  ---RYFLNSVIVSVITAILVTMIAAAAGYAMSRFSFRGKTTVAVTLLLTQTFPLVMVIPP 130

Query: 140 LYALFDRLGQYVPFVGLNTHGGVIFAYMG-GIALHVWTIKGYFETIDGSLEEAAALDGAT 198
           +Y +  +LG        N+  G+I  Y    IA   + ++ +F+ I   LEEAA +DG +
Sbjct: 131 MYRIMGQLGL------TNSLTGLIIIYTAFNIAFATFLMQSFFDGIPKDLEEAAMIDGCS 184

Query: 199 PWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNY 258
             QA R +++PL++P +       F AA +E+  A +L+   +  T AVG+  ++     
Sbjct: 185 RSQALRKIIIPLTLPGMGATLGFVFTAAWSELLFALMLISSDSQKTFAVGLLTFIGKFAV 244

Query: 259 LWGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296
            WG   AA+VL+ IP  + F   QR+LV GLTAG VKG
Sbjct: 245 DWGQMMAASVLALIPACLFFAFLQRYLVTGLTAGAVKG 282


Lambda     K      H
   0.328    0.141    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: 238
Number of extensions: 14
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: 296
Length of database: 282
Length adjustment: 26
Effective length of query: 270
Effective length of database: 256
Effective search space:    69120
Effective search space used:    69120
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 24 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