GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Skermanella stibiiresistens SB22

Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate WP_037455934.1 N825_RS19885 maltose alpha-D-glucosyltransferase

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



>NCBI__GCF_000576635.1:WP_037455934.1
          Length = 1104

 Score =  246 bits (628), Expect = 3e-69
 Identities = 175/548 (31%), Positives = 264/548 (48%), Gaps = 103/548 (18%)

Query: 1   MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60
           +W+K+AVIYQ++ ++F D + DG+GD  G+ ++L YL+ LGV ALWL PFY SP++D GY
Sbjct: 8   LWYKDAVIYQLHVKAFFDADNDGIGDFAGLSQKLDYLQELGVTALWLLPFYPSPLRDDGY 67

Query: 61  DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASR-NSPK 119
           D+ADY +V+P +G ++DF + + E H+ G++V+ +LV NHTS +HPWF  +R ++  S  
Sbjct: 68  DIADYRNVNPSYGFMKDFRQFVRECHSRGMRVITELVINHTSDQHPWFQRARTAKPGSNH 127

Query: 120 RDWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAI 179
           R++Y+W D                   WT D     Y+ H+F   QPDLN+ NP V   +
Sbjct: 128 RNFYVWSDSDQKYQGTRIIFLDTEKSNWTWDPVAKSYFWHRFYSHQPDLNFDNPAVLREV 187

Query: 180 YEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETY 239
             V+RFWL  GVDG R+D +  L E    R+   N                  E+  ET+
Sbjct: 188 LSVLRFWLDMGVDGLRLDAVPYLIE----REGTNN------------------ENLSETH 225

Query: 240 AYVREMRQVLDEFSEPGRERVMVGEI------YLPYPQLVRYYQAGCHLPFNFHL---IF 290
             ++++R  +D   E   +R+++ E        LPY   +      CH+ F+F L   ++
Sbjct: 226 DILKQIRAAVD---EGYADRMLLAEANQWPEDVLPYFGDLSKGGDECHMAFHFPLMPRMY 282

Query: 291 RGLPDWRPENLARIVEEYESLLTRWDWPNWVLGNHDQ----------------------- 327
             +       +  I+ +   +     W  + L NHD+                       
Sbjct: 283 MAIAQEDRHPVTDIMRQTPEIPETCQWAVF-LRNHDELTLEMVTDKERDYLWNFYAKDRR 341

Query: 328 --------PRLASRLGEAQARVAAM--LLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPA 377
                    RLA+ +   + ++  +  LLF++ GTP  YYGDEIGM              
Sbjct: 342 MRINLGIRRRLATLMDNDRRKIELLNSLLFSMPGTPVVYYGDEIGM-------------- 387

Query: 378 ALRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEP---WLPVNPD----YKTRNVA 430
                   G++     RD  RTPMQW      GFS  +P   +LP   D    +   NV 
Sbjct: 388 --------GDNVYLGDRDGVRTPMQWSPDRNGGFSRSDPARLYLPAVADPIYGFDAVNVE 439

Query: 431 AQEQDPRSMLHLVRRLIALRKDPDLL-YGAYR-TYRAREGVYAYLR---GEGWLVALNLT 485
           AQE+ P S+L+ ++RLIA+R+       GA R  Y     V AYLR   GE  L   NL+
Sbjct: 440 AQERSPSSLLNWMKRLIAVRQQQKSFGRGALRFLYPGNRKVLAYLREHEGEVILCVANLS 499

Query: 486 EKEKALEL 493
              +A+EL
Sbjct: 500 RSAQAVEL 507


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: 1781
Number of extensions: 91
Number of successful extensions: 5
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: 528
Length of database: 1104
Length adjustment: 40
Effective length of query: 488
Effective length of database: 1064
Effective search space:   519232
Effective search space used:   519232
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: 55 (25.8 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