GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Caldicellulosiruptor kronotskyensis 2002

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate WP_013431305.1 CALKRO_RS12210 PTS transporter subunit EIIC

Query= TCDB::P71012
         (635 letters)



>NCBI__GCF_000166775.1:WP_013431305.1
          Length = 454

 Score =  443 bits (1139), Expect = e-129
 Identities = 238/463 (51%), Positives = 328/463 (70%), Gaps = 19/463 (4%)

Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230
           KI+AVT+CPTGIAHT+MAA+AL+  AKELGVEIKVET GS G ++++T +++++A A+I+
Sbjct: 3   KIVAVTSCPTGIAHTYMAAEALQMAAKELGVEIKVETRGSVGAENEITPEDLKEAHAVIL 62

Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAK 290
           A D +++ +RF+G  +++  V   I+ P+ LI KAMN +   Y             +EAK
Sbjct: 63  ACDTKIDEDRFQGLPIVRASVKDAIKDPKGLITKAMNMEKKDYVDK-----VFEAKKEAK 117

Query: 291 GKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNF 350
            K+ +G+    YKHLM+GVS M+PFVV GGIL+AISF +GI + +       T AAAL  
Sbjct: 118 EKA-TGV----YKHLMTGVSYMIPFVVAGGILIAISFAFGIKAFEKK----GTLAAALMD 168

Query: 351 IGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVI 410
           IGG +A  L+V +LAGFIA SIADRPG  PGM+GG +A +  AGFLGG++AGF AGY+V 
Sbjct: 169 IGGGSAFYLMVPILAGFIAFSIADRPGLVPGMIGGLLANKLGAGFLGGIVAGFAAGYLVA 228

Query: 411 LLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGN 470
            LKK    +P++++GL PVLI P+    I G+ M +VV  PVAA    +T WL+S+ +G+
Sbjct: 229 WLKKTIK-LPKTMEGLMPVLILPVLSTLIIGLGMIYVVGEPVAALNKAMTEWLKSMSSGS 287

Query: 471 LVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAP-HAAIMAGGMVPPLGIALATT 529
            VL+GIILG MMA DMGGP+NKAA+TF ++ + AG  +   AA+MA GM PPLG+ALAT 
Sbjct: 288 AVLLGIILGLMMAFDMGGPVNKAAYTFAVSTLAAGQPSTIMAAVMAAGMTPPLGLALATL 347

Query: 530 IFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRV 589
           I ++KFT  +REAG   +F+G +F+TEGAIPFAAADPLRVIP+ ++G+AV   L+  F+ 
Sbjct: 348 IAKDKFTTEEREAGKAAFFLGISFITEGAIPFAAADPLRVIPSIMIGSAVTSALSILFKC 407

Query: 590 TLPAPHGGVFVAFITN---HPMLYLLSIVIGAVVMAIILGIVK 629
           TL  PHGG+FV  I N   + +LY ++I IG VV A+I+ ++K
Sbjct: 408 TLAVPHGGIFVLPIPNAVGNLLLYAVAIAIGTVVTALIVSVLK 450


Lambda     K      H
   0.320    0.137    0.390 

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: 719
Number of extensions: 29
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: 635
Length of database: 454
Length adjustment: 35
Effective length of query: 600
Effective length of database: 419
Effective search space:   251400
Effective search space used:   251400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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