GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Cronobacter condimenti 1330

Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate WP_007678620.1 BN137_RS04085 alpha,alpha-phosphotrehalase

Query= CAZy::AAS80455.1
         (528 letters)



>NCBI__GCF_000319285.1:WP_007678620.1
          Length = 551

 Score =  342 bits (878), Expect = 2e-98
 Identities = 211/561 (37%), Positives = 309/561 (55%), Gaps = 60/561 (10%)

Query: 2   WWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 61
           WW+  VIYQ+YP+SFQDT+G+G GDL GV +RL YL +LG+DA+WL+PFY SP  D GYD
Sbjct: 7   WWQNGVIYQIYPKSFQDTSGNGTGDLAGVIQRLDYLHTLGIDAIWLTPFYLSPQVDNGYD 66

Query: 62  VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 121
           VA+Y  +DP +GTL +FD L+ EAHA G++V++D+V NHTS++H WF ++  +R S  R+
Sbjct: 67  VANYTAIDPAYGTLDEFDTLVSEAHARGIRVVLDMVFNHTSTQHAWFHDA-LTRESAHRN 125

Query: 122 WYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIYE 181
           +YIW+D  P+   PNNW+S FGG AW     +GQYYLH F PEQ DLNW NP+VR+ + +
Sbjct: 126 FYIWRDGTPEEA-PNNWRSKFGGSAWRWHAESGQYYLHLFAPEQADLNWENPQVRDEVKK 184

Query: 182 VMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYAY 241
           V  FW  RGVDG R+DV+ L+++D   +D P +        DRG     +T D P  + Y
Sbjct: 185 VCEFWADRGVDGLRLDVINLISKD---QDFPAD--------DRGDGRRFYT-DGPRIHDY 232

Query: 242 VREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQA----GCHLPFNFHLIFRGLPDWR 297
           ++E+ +  D F   G   + VGE+     +  + Y A       + FNFH +    P+ +
Sbjct: 233 LQELSR--DVFVPRG--LMTVGEMSSTTLENCQRYAALEGHELSMTFNFHHLKVDYPNGQ 288

Query: 298 PENLAR--------IVEEYESLLTRWDWPNWVLGNHDQPRLASRLGE------AQARVAA 343
              LA+        I   ++  +    W      NHDQPR+ SR G+        A++ A
Sbjct: 289 KWTLAQPDFVALKAIFNHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGALRVPAAKMLA 348

Query: 344 MLLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAALRQKDRLGEHN-------------L 390
           M+L  ++GTP  Y G+E+GM N      ++ D   +   +   E                
Sbjct: 349 MVLHGMQGTPYIYQGEELGMTNPHF--TRIVDYRDVESHNMFAERRAQGQSPETLLAILA 406

Query: 391 PPGRDPERTPMQWDDTPFAGFSTVEPWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALR 450
              RD  RTPMQWDD+   GF+T  PW+ +  +Y+  N A   +DP S+ +  ++LIALR
Sbjct: 407 SKSRDNGRTPMQWDDSDNGGFTTGTPWIGLCDNYREINAARALEDPDSVFYAYQKLIALR 466

Query: 451 K-DPDLLYGAYRTYRA-REGVYAYLR---GEGWLVALNLTEKEKAL---ELPRGGRVVLS 502
           K  P   +G Y+   A    ++ Y R   G+  +V  NL+ +       +     + ++S
Sbjct: 467 KAHPIFTWGDYQDLLAGHPYLWCYRREWQGQQMVVVANLSREAHWCTPGDFTGEWQTLMS 526

Query: 503 THLDREERVGERLFLRPDEGV 523
            + D     GE + LRP E V
Sbjct: 527 NYPDAAPAPGE-INLRPFEAV 546


Lambda     K      H
   0.321    0.141    0.466 

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: 1081
Number of extensions: 65
Number of successful extensions: 6
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: 528
Length of database: 551
Length adjustment: 35
Effective length of query: 493
Effective length of database: 516
Effective search space:   254388
Effective search space used:   254388
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