GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcF in Sinorhizobium fredii NGR234

Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= TCDB::Q8RJU9
         (308 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  121 bits (303), Expect = 2e-32
 Identities = 91/302 (30%), Positives = 149/302 (49%), Gaps = 22/302 (7%)

Query: 1   MQHGKYRFIVGFLAVPLGLYAL-LVVWPFIQSIYYSFTDWTGLSPD--FKTVGFDNYERM 57
           ++H   R +   +  P  L  L L ++P I  ++Y+       +PD  ++ VG  N+ R+
Sbjct: 19  LEHWAERHLRYLMLAPTVLILLALTIFPSIY-MFYAAVHRISPNPDLPWEFVGVGNFARL 77

Query: 58  LDDDIFWKSLQHSLLFALLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIV 117
           L D  F  +L+++++F L+   +   L L  A +++              +R   F K V
Sbjct: 78  LSDPQFHVALRNTVVFTLVAVALEFLLGLGLALLLD------------RFIRRLSFLKTV 125

Query: 118 YFFPQVLSIAIVALLFAFAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVW 177
              P +L    VA+ +   Y P  G +N ++  +GL  VQ  W GD +LA++ ++   VW
Sbjct: 126 LMIPMMLPPIAVAITWKLIYEPQFGVLNEIMFLLGL-PVQ-AWAGDVNLAMFSIIVADVW 183

Query: 178 STVGFFVVLFSAGMASIPADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILAL 237
               F  +L  AG+AS+P + YEAA LDGA+    F+ +TLP L   +    +   + AL
Sbjct: 184 QWTPFVFLLMLAGLASLPVEPYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDAL 243

Query: 238 GAESFAVVHIMTTGPGGPDYSTTVMVLYVYQKAFRDGQAAYATTIGVALLIVTLAFAAVV 297
               F +V I+T   GGP   T V+ LY+YQ A+R     YA  I + +L VT+  +   
Sbjct: 244 --RLFDLVFILT--GGGPADRTKVLSLYIYQVAYRFADPGYAAAISLFVLFVTIVLSTWF 299

Query: 298 MR 299
           M+
Sbjct: 300 MK 301


Lambda     K      H
   0.330    0.145    0.458 

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: 245
Number of extensions: 12
Number of successful extensions: 3
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: 308
Length of database: 307
Length adjustment: 27
Effective length of query: 281
Effective length of database: 280
Effective search space:    78680
Effective search space used:    78680
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 Apr 09 2024. 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