GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Chryseobacterium viscerum 687B-08

Align MFS transporter (characterized, see rationale)
to candidate WP_103234339.1 C1634_RS22640 MFS transporter

Query= uniprot:A0A1X9ZCC9
         (458 letters)



>NCBI__GCF_002899945.2:WP_103234339.1
          Length = 468

 Score =  317 bits (812), Expect = 5e-91
 Identities = 172/464 (37%), Positives = 270/464 (58%), Gaps = 32/464 (6%)

Query: 10  PKLTLVQIINMSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQPI 69
           PKL+  QI NM+VGFFGIQ+ + LQ+  +  +Y  LGA+ DQ+P+L LA P+TGLL+QP+
Sbjct: 7   PKLSFWQIWNMNVGFFGIQYSFGLQQTAVNPLYSFLGAHADQLPILNLAGPVTGLLIQPL 66

Query: 70  IGYLSDRTWHPKWGRRRPYFMIGAIVSSIALIFMPHSSVLWMAAGLLWILDVFGNIAMEP 129
           IG +SD+TW  KWGRR+P+F++GA+  S+AL   P SS +WMA GLLWILD   N AMEP
Sbjct: 67  IGAISDKTWSVKWGRRKPFFLLGAVFCSLALFVFPFSSSIWMAVGLLWILDAANNTAMEP 126

Query: 130 FRAFVTDKLPDSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAEQGSIPENVKF 189
           +RAF+ DKLP+ Q   GF MQS+ +G G ++A+   +     F    ++E G IP  V +
Sbjct: 127 YRAFIGDKLPEEQQTYGFQMQSLFVGGGITLANLSLFAFQKYF--GGSSESGGIPAWVYY 184

Query: 190 SFYIGAFFFFAAVLWTVFTTKEYPPQDVD-FKEKVKESNKGFGGGAREIFHALRNMPKRM 248
           SF++G+F   A+V+W+V+ T E PP + +  K K ++ N        +IF A+  MPK +
Sbjct: 185 SFFLGSFCSIASVVWSVYKTPEIPPTEEELIKLKAEKENDTVFTPFVDIFTAIIKMPKIL 244

Query: 249 QIVSLVQFFTWPGLFLMWFYYTTAVAVNVFGGKDA--------------------ADPVY 288
             ++LV  F W  LF  W + T  +   ++   ++                    +D  +
Sbjct: 245 WQLALVYLFQWYALFCYWQFVTPMIKQTLYHVSESDEQKANHFIELSKNGLSVSQSDMSW 304

Query: 289 AQ--------GADFGSLTLAYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISV 340
           A+              L   +Y+ IT + AL+L   A     K  +  CL    I L+ +
Sbjct: 305 AKNILNLVETAVGQTGLMNGFYNFITMISALMLIPFALKYSSKNVYVFCLSATGISLLIL 364

Query: 341 AWVHDKNMLYLCMTGVGIAWASILSMPYAMLSGSLPKDKIGIYMGIFNFFIVLPEIIASL 400
            ++H++ ++ L M   GI WA+++ +PY+M+S S+P +K G+YMG+ N  IV+P +I ++
Sbjct: 365 PFIHNEYLILLPMVLFGIGWAAMMGLPYSMVSPSIPAEKRGVYMGVINMMIVIPMLIQTV 424

Query: 401 GFGWLMRNVLNNDRLLAVQLGGGLMILAAVICYVFIREPKKTDE 444
            FG++ +N L +D   A+ + G L +LA+ I  + I+  + TD+
Sbjct: 425 SFGFIYKNFLGSDPSNAITMAGTLFLLAS-ISVMLIQVKRSTDQ 467


Lambda     K      H
   0.327    0.142    0.448 

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: 637
Number of extensions: 34
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: 458
Length of database: 468
Length adjustment: 33
Effective length of query: 425
Effective length of database: 435
Effective search space:   184875
Effective search space used:   184875
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: 51 (24.3 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