GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Rhizobium freirei PRF 81

Align LacF, component of Lactose porter (characterized)
to candidate WP_004127663.1 RHSP_RS29500 sugar ABC transporter permease

Query= TCDB::P29823
         (298 letters)



>NCBI__GCF_000359745.1:WP_004127663.1
          Length = 286

 Score =  224 bits (572), Expect = 1e-63
 Identities = 117/284 (41%), Positives = 174/284 (61%), Gaps = 5/284 (1%)

Query: 16  NGWLFVAPAIALISVFMLYPILRSLVLSLYTGRGMMLKFSGTGNLVRLWNDPVFWQALQN 75
           + + F+AP + + + F ++PI+ S ++S    R     ++ + N  RL+ DP F+ ALQN
Sbjct: 7   SAYAFLAPYLLVFAAFWVWPIIDSFLISFQNTRVNPWVYNLSLNWGRLFGDPAFYNALQN 66

Query: 76  TVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAYSILFKSMFSLD 135
           T+I  +VQVP+MIT+A ++A +LN+P L+  G+FR   F P V   VAY+ +F+ MF++D
Sbjct: 67  TLIILIVQVPVMITLATVMAVLLNSPLLKARGIFRFAFFAPVVVGEVAYAAVFRLMFNVD 126

Query: 136 -GVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDRSIYE 194
            G+VN  L  +G    P+ W  +   A VLIIIA+TWRW GYN I  L+ LQ+I   +YE
Sbjct: 127 FGIVNKLLGTVGFA--PVSWFAESHAAMVLIIIAVTWRWAGYNAIIILSGLQSIPEDVYE 184

Query: 195 AAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANSTLTL 254
           AA +D V  + +F  +T+P+LKP+ILF  + S IGT+QLF E Y  T   GGP   T TL
Sbjct: 185 AATLDRVNRFQQFIHITLPLLKPIILFCVVLSVIGTMQLFTEPYLIT-NRGGPGGGTETL 243

Query: 255 SLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAARERK 298
            L +Y   F+   +F YA+ V+Y +  +   +S L  +  RE K
Sbjct: 244 GLLLYRQAFQ-STNFGYASAVAYTMAALAVAISLLNLWVGREPK 286


Lambda     K      H
   0.329    0.141    0.435 

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: 290
Number of extensions: 19
Number of successful extensions: 4
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: 298
Length of database: 286
Length adjustment: 26
Effective length of query: 272
Effective length of database: 260
Effective search space:    70720
Effective search space used:    70720
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.

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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