GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Rhizobium freirei PRF 81

Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate WP_004129777.1 RHSP_RS32465 ribose ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21390
         (340 letters)



>NCBI__GCF_000359745.1:WP_004129777.1
          Length = 320

 Score =  251 bits (640), Expect = 2e-71
 Identities = 151/338 (44%), Positives = 202/338 (59%), Gaps = 24/338 (7%)

Query: 1   MNAILENKPAMAPAKSRRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMI 60
           MN I   KP    A    R   + SI LV     L+   F +      + M     + ++
Sbjct: 1   MNTIAAAKPGNFRAGEMIR---QFSIVLVFF---LIVAFFAFA---NQYFMTWLNWLNLV 51

Query: 61  LQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW 120
            Q SI G+LAIGVT VI+T GIDLS GSV+AL+ MIAASL   ++    +F         
Sbjct: 52  RQSSINGILAIGVTFVILTKGIDLSVGSVMALAGMIAASLVTETNEQFVLFG-------- 103

Query: 121 IPVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT 180
             + AGL  G   G +NG ++A   +PPF+ TLGM+  ARGL   ++EG+P+  LSD + 
Sbjct: 104 --IFAGLAAGAGLGLVNGVLVAAVKVPPFVVTLGMLSVARGLTLIFSEGRPIPNLSDPFK 161

Query: 181 AIGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVI 235
            IG G +     P++I  VV +I    L YT +G+Y YA+GGN +AARTSGI+ K  +  
Sbjct: 162 WIGSGQIMYIPVPIVILFVVFLIGWTVLNYTTFGRYVYAVGGNEKAARTSGISTKVIVGA 221

Query: 236 VYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295
            Y I+GLLAGLAG+V +AR        G+ YELDAIAA VIGGTSLAGG G + GT+IGA
Sbjct: 222 TYVISGLLAGLAGLVLTARTTAALPQAGIGYELDAIAAVVIGGTSLAGGRGSLLGTLIGA 281

Query: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYR 333
           LI+G + +G   +GV +Y Q ++KG IIV+AV+ DQ R
Sbjct: 282 LIIGTINNGMDLMGVSSYYQQVLKGTIIVVAVIADQIR 319


Lambda     K      H
   0.326    0.140    0.394 

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: 293
Number of extensions: 17
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: 340
Length of database: 320
Length adjustment: 28
Effective length of query: 312
Effective length of database: 292
Effective search space:    91104
Effective search space used:    91104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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