GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Mariniradius saccharolyticus AK6

Align MFS transporter (characterized, see rationale)
to candidate WP_157198615.1 C943_RS18350 MFS transporter

Query= uniprot:A0A1X9ZCC9
         (458 letters)



>NCBI__GCF_000330725.2:WP_157198615.1
          Length = 427

 Score =  414 bits (1065), Expect = e-120
 Identities = 207/427 (48%), Positives = 287/427 (67%), Gaps = 3/427 (0%)

Query: 20  MSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQPIIGYLSDRTWH 79
           MS GF GIQFG+ LQ   M RI++ LGA+ D +PLL++AAPLTGLLVQPI+GYLSDRTWH
Sbjct: 1   MSFGFLGIQFGFALQGGFMSRIFQTLGADKDAIPLLWIAAPLTGLLVQPIVGYLSDRTWH 60

Query: 80  PKWGRRRPYFMIGAIVSSIALIFMPHSSVLWMAAGLLWILDVFGNIAMEPFRAFVTDKLP 139
            ++GRRRP+F+IGA++S+IAL F P+SS LWMAAG LWILD   NI+MEPFRA V DKLP
Sbjct: 61  SRFGRRRPFFLIGAVMSTIALFFAPYSSALWMAAGALWILDASINISMEPFRALVADKLP 120

Query: 140 DSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAEQGSIPENVKFSFYIGAFFFF 199
           DSQ + GF++Q+++IG+G  VAS LPW M  +  + NTAE G +P++VKF+F +GA   F
Sbjct: 121 DSQRSYGFVVQTLIIGIGTWVASNLPWFMTQI-GIPNTAEAGVVPDSVKFAFAVGAVVLF 179

Query: 200 AAVLWTVFTTKEYPPQDVDFKEKVKESNKGFGGGAREIFHALRNMPKRMQIVSLVQFFTW 259
            ++L+T+ TT EYPP+D+D  ++  E +KGF  G +EIF  +  MP  M+ + +VQFF+W
Sbjct: 180 GSILYTILTTDEYPPEDLDAFKRENEESKGFINGLQEIFKNIAGMPPVMKQLGIVQFFSW 239

Query: 260 PGLFLMWFYYTTAVAVNVFGGKDAADPVYAQGADFGSLTLAYYSVITFLFALVLPKIAD- 318
              F MW + T A+  +VF   D    VY   AD     L  Y +++  FAL+L  +   
Sbjct: 240 FAFFTMWSFATPAITEHVFKATDTTSQVYNDAADSVGNYLGTYGLVSMFFALILAFVTSK 299

Query: 319 -ALGRKTTHALCLICGAIGLISVAWVHDKNMLYLCMTGVGIAWASILSMPYAMLSGSLPK 377
             + RK  H L LI G +G IS+ +V    ML+LC   VG+AWASILSMPYAMLS ++  
Sbjct: 300 VKINRKMVHMLSLIAGGVGFISIYFVQTPWMLHLCFALVGVAWASILSMPYAMLSSAVNP 359

Query: 378 DKIGIYMGIFNFFIVLPEIIASLGFGWLMRNVLNNDRLLAVQLGGGLMILAAVICYVFIR 437
            ++G+YMGIFN FIV+P+I+A+LG       +L  + ++   +  G  ++ A +  + I 
Sbjct: 360 KQMGVYMGIFNMFIVIPQIVAALGGINFSYKLLFGEEVIYTMVLAGTSLIIAGLANLLIT 419

Query: 438 EPKKTDE 444
           +   T +
Sbjct: 420 DRSATHD 426


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: 663
Number of extensions: 33
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: 458
Length of database: 427
Length adjustment: 32
Effective length of query: 426
Effective length of database: 395
Effective search space:   168270
Effective search space used:   168270
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