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_109738207.1 C1634_RS08215 MFS transporter

Query= uniprot:A0A1X9ZCC9
         (458 letters)



>NCBI__GCF_002899945.2:WP_109738207.1
          Length = 467

 Score =  310 bits (793), Expect = 8e-89
 Identities = 168/449 (37%), Positives = 260/449 (57%), Gaps = 31/449 (6%)

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

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

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

Query: 190 SFYIGAFFFFAAVLWTVFTTKEYPPQDVDFKE-KVKESNKGFGGGAREIFHALRNMPKRM 248
           SF++G+F   A+V+W+V+ T E PP D +  + K ++ N        +IF A+ NMPK +
Sbjct: 185 SFFLGSFCSVASVVWSVYKTPEIPPTDEELIQLKAEKENDTVFTPFIDIFKAIVNMPKIL 244

Query: 249 QIVSLVQFFTWPGLFLMWFYYTTAVAVNVFGGKDAADP---------------------- 286
             ++LV  F W  LF  W + T  +   ++   +  +                       
Sbjct: 245 WQLALVYLFQWYALFCYWQFATPMIKQTLYHVSEIDEERANRFVELSKNGFSVPQNDLLW 304

Query: 287 ------VYAQGADFGSLTLAYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISV 340
                 +  Q      L   +Y+ IT + AL+L   A     K  +A CL+   I L+ +
Sbjct: 305 AKNILHLVEQAVGQTGLMNGFYNFITMISALLLIPFALKFSAKNVYAFCLLATGISLLVL 364

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

Query: 401 GFGWLMRNVLNNDRLLAVQLGGGLMILAA 429
            FG   + +L ++   A+++ G L +LA+
Sbjct: 425 TFGAFYKYILGSNPADAIRIAGILFLLAS 453


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: 655
Number of extensions: 34
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 458
Length of database: 467
Length adjustment: 33
Effective length of query: 425
Effective length of database: 434
Effective search space:   184450
Effective search space used:   184450
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