Alignments for a candidate for treF in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Stenotrophomonas chelatiphaga DSM 21508

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate WP_083491891.1 ABB28_RS03155 glycoside hydrolase family 15 protein

Query= CAZy::ABK72415.1
         (668 letters)



>NCBI__GCF_001431535.1:WP_083491891.1
          Length = 613

 Score =  233 bits (594), Expect = 2e-65
 Identities = 191/632 (30%), Positives = 287/632 (45%), Gaps = 74/632 (11%)

Query: 41  PIADYGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDR-GAGHFRLGPYGVSVPA 99
           PI  Y  L +  +  L    GS++W C P  DSP +F  +LD    G+F + P       
Sbjct: 31  PIEQYSALGEGRSVALTGCDGSIDWWCAPNMDSPPLFDRLLDATNGGYFSIAPTEPCT-V 89

Query: 100 ARRYLPGSLILETTWQTHTGWLIVRDALVMG-----PWHDIDTRSRTHRRTPMDWDAEHI 154
            RRY   S +LET + T +G   + ++L  G     PW +                    
Sbjct: 90  ERRYRAESNVLETVFTTASGRASLTESLNSGNAGRLPWCE-------------------- 129

Query: 155 LLRTVRCVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTN 214
           L R +  + G V   +   P       S      G      + R       HP L+L   
Sbjct: 130 LARRIEGLEGEVRFAVRMCPGTRAQSASPYCSSIGEHVVFHVQRLLGVMIHHPALQLQWT 189

Query: 215 LRIGIEGREARARTRLTEGDNVFVALSWSKHP---APQTYE-----EAADKMWKTSEAWR 266
                    A     ++ G  V VAL   +     AP   E     +  D+ WK   AW 
Sbjct: 190 ------DEGASGECTVSAGGRVTVALVVGEDEPLVAPSVEEVDGRIDLTDREWK---AWA 240

Query: 267 QWINVGDFPDHPWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWI 326
           + ++ G +     RA   RS L LK L YSP+GA+ AA TTSLPE   G++N+DYRY+W+
Sbjct: 241 RNVSYGGWD----RATFVRSTLALKLLLYSPSGAIAAAATTSLPERIGGDKNFDYRYAWV 296

Query: 327 RDSTFALWGLYTLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHL 386
           RD+ + +      GL+ E+   F+++          RH  +V++ + GE+    +EL  +
Sbjct: 297 RDAGYTIQAFLAAGLEAESKAAFTWL-----LRQLRRHGPKVVFTLDGEKVEPVQEL-PM 350

Query: 387 SGYDNSRPVRIGNGAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHW 446
            GY NS+PV  GN A  Q QH I+G + ++ +    +   +  A   +L    +    HW
Sbjct: 351 HGYRNSQPVVKGNLAGEQHQHGIYGDIFETAFCFVAAGNILDGASAELLSRIADLCADHW 410

Query: 447 KEPDRGIWEVRGEPQHFTSSKIMCWVALDRGSKLAELQGE--KSYAQQWR----AIAEEI 500
           +  D GIWE+  E +H+T SKI CW AL R  +LA+ QG+   +   +W+     I+E I
Sbjct: 411 RAKDSGIWEL-PELEHYTMSKISCWQALARAVELAD-QGQLPTTCRDRWQRERDRISEWI 468

Query: 501 KADVLARGVDKRGVLTQRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGL 560
           + +  +   D         G   LDA+L LAV  RF   D  R+ AT+ AI  EL + G 
Sbjct: 469 ETNCWS---DSLQAYEMYPGSGRLDAALALAVRFRFDGRD--RLLATLRAIDRELGQSGF 523

Query: 561 VLRYRVEETDDGLAGEEGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLH-LYAE 619
             RY       G+A EEG F  CS+W+  A   +G ++ A+   + L         + +E
Sbjct: 524 HYRY------SGMAEEEGCFIACSYWMAEAYARLGFVADARDRVDALNGALGRCQGVLSE 577

Query: 620 EIEPRTGRHLGNFPQAFTHLALINAVVHVIRA 651
            ++P TG +LGN PQ  +HLA + A+  +  A
Sbjct: 578 MVDPATGHYLGNTPQGLSHLAQVMAMATIADA 609


Lambda     K      H
   0.319    0.135    0.426 

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: 1107
Number of extensions: 60
Number of successful extensions: 8
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: 668
Length of database: 613
Length adjustment: 38
Effective length of query: 630
Effective length of database: 575
Effective search space:   362250
Effective search space used:   362250
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources