GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_04205 in Amantichitinum ursilacus IGB-41

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate WP_083458844.1 WG78_RS07235 MFS transporter

Query= reanno::WCS417:GFF828
         (454 letters)



>NCBI__GCF_001294205.1:WP_083458844.1
          Length = 444

 Score =  380 bits (975), Expect = e-110
 Identities = 190/433 (43%), Positives = 269/433 (62%), Gaps = 15/433 (3%)

Query: 5   KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64
           KPT  RYL L+M+F+   I Y DRA +A+A + +QK+ GI    +GYIFSAF W Y A Q
Sbjct: 22  KPTRRRYLTLVMIFITVVICYVDRANLAVASAHIQKEFGISRAQMGYIFSAFAWTYTACQ 81

Query: 65  IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSF 124
           IPGGW LDR GSK  Y +++  WS+ T+ QG+ G       + +L  LR + GL EAP+F
Sbjct: 82  IPGGWFLDRVGSKLTYFIAVMGWSVATLFQGFAG------GLASLVGLRAITGLFEAPAF 135

Query: 125 PGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGII 184
           P N R+V +WFP  ER +A   + S Q+       PL+ WI  S  W  VFI  G +GII
Sbjct: 136 PTNNRMVTSWFPEQERASAVGFYTSGQFVGLAFLTPLLIWIQESLSWHWVFIATGAVGII 195

Query: 185 FSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQ---DKGKGKKTDGPKWDYIRQLL 241
           ++L+W  V   PR+   IN+AE +HIAA G M+D D     K +GK T    W    +L+
Sbjct: 196 WALVWHFVYQPPRKSRGINQAELDHIAAGGGMIDGDAPSTQKSRGKVT-AADW----KLI 250

Query: 242 TNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGG 301
            NR ++GVY+GQ+ I    +FFLTWFP YL Q++ ++ L AGF+ ++P +  F+G +L G
Sbjct: 251 FNRKLVGVYVGQFAIASTLWFFLTWFPSYLTQEKHVSALTAGFMTTVPFLAAFVGVLLSG 310

Query: 302 VISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALG 361
             +D ++R G S+ FARK PII GLL+S+ I+  NY +    ++  MA+AFFG G  ++ 
Sbjct: 311 FAADRMVRAGKSIGFARKLPIISGLLLSTCIIGANYTEDPVWIMTLMAIAFFGNGFASIT 370

Query: 362 WAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAV 421
           W++VS  +P ++ GL+GG+FN  G L  IT P+VIGYI    G F  AL ++   AL+  
Sbjct: 371 WSLVSSLAPLRLIGLTGGVFNFVGGLGGITVPLVIGYIAQDYG-FAPALAYISVVALIGA 429

Query: 422 FSYLVIVGPIKRV 434
            SY+ +VG ++RV
Sbjct: 430 LSYIFLVGEVRRV 442


Lambda     K      H
   0.327    0.142    0.444 

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: 725
Number of extensions: 49
Number of successful extensions: 5
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: 454
Length of database: 444
Length adjustment: 33
Effective length of query: 421
Effective length of database: 411
Effective search space:   173031
Effective search space used:   173031
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