Alignments for a candidate for treF in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Sulfuritalea hydrogenivorans DSM 22779

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate WP_041099027.1 SUTH_RS10195 glycoside hydrolase family 15 protein

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



>NCBI__GCF_000828635.1:WP_041099027.1
          Length = 592

 Score =  269 bits (688), Expect = 2e-76
 Identities = 203/629 (32%), Positives = 304/629 (48%), Gaps = 59/629 (9%)

Query: 44  DYGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDRGAGHFRLGPYGVSVPAARR- 102
           D   + +C    LI +   + W C PR D   VF ++L R A  +  G   V +    R 
Sbjct: 5   DLAMIGNCTVGALIDARAKIVWGCFPRFDGDPVFCSLL-RNADDY--GYAAVELADCERT 61

Query: 103 ---YLPGSLILETTWQT-HTGWLIVRD-ALVMGPWHDIDTRSRTHRRTPMDWDAEHILLR 157
              YL  + IL T     H G + + D A   G +       R  R  PM      +L+R
Sbjct: 62  EQHYLENTAILLTRLHDCHGGGVEITDFAPRFGQY------GRMFR--PM------MLVR 107

Query: 158 TVRCVSGTVELVMSCEPAFD--YHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTNL 215
            +R + G+  L +   PA D    R   TW   G  +   +A          TLRLTT+ 
Sbjct: 108 RIRRLGGSPRLTLRLRPACDDGAARPEVTW---GSNHIRYVAPGL-------TLRLTTDA 157

Query: 216 RIGIEGREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWK-----TSEAWRQWIN 270
            +    +E    T     D V + L      A ++  EAA ++ +     T++ WR+W+ 
Sbjct: 158 SLTAILQE----TPFFLEDTVTLLLG-----ADESVHEAAGEVGRRFFEETAQYWREWVR 208

Query: 271 VGDFPDHPWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDST 330
               P + W+  + R+A+TLK   +  TGA++AA TTS+PE     RNWDYRY W+RD  
Sbjct: 209 FLGIP-YEWQEAVIRAAVTLKLNAFDDTGAIVAAMTTSIPEAAGSSRNWDYRYCWLRDGY 267

Query: 331 FALWGLYTLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYD 390
           F +  L  LG  R  + + ++I +V  A N     LQ +YG+ G   L E E+  L GY 
Sbjct: 268 FVVNALNRLGATRSMERYIAYIVNV--AANAAGGALQPVYGIDGRADLAEREVDALPGYR 325

Query: 391 NSRPVRIGNGAYNQRQHDIWGTML---DSVYLHAKSREQIPDALWPVLKNQVEEAIKHWK 447
              PVRIGN AY Q QHD++G+ +     ++   +   +  +AL+  L+   E+A + + 
Sbjct: 326 GMGPVRIGNQAYRQVQHDVYGSAILAATHIFFDQRLTRRGDEALFHRLEALGEQARRCYD 385

Query: 448 EPDRGIWEVRGEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR 507
           +PD G+WE+RG  +  T S +MCW A DR  ++A   G    A  W   ++++   +  R
Sbjct: 386 QPDAGLWELRGSARVHTFSAVMCWAACDRLGRIAARLGLAERAAYWSEYSKQMHETISRR 445

Query: 508 GVDK-RGVLTQRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRV 566
             +K R      +   A+DASLLL     FL   DPR  ATV A+  +L     + RY V
Sbjct: 446 AWNKRRNAFVSTFDGKAMDASLLLLAEVGFLDVADPRFAATVAAVEKDLRHGDFIFRY-V 504

Query: 567 EETDDGLAGEEGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTG 626
           E+ D G    E  F +C+FW V+AL  +     A+ L ERLL+  +   L AE I+P+TG
Sbjct: 505 EKDDFG--KPENAFLVCTFWYVNALAALDRRDEARALFERLLACRNQHGLLAEHIDPKTG 562

Query: 627 RHLGNFPQAFTHLALINAVVHVIRAEEEA 655
              GNF Q ++ + LINA + +    ++A
Sbjct: 563 EQWGNFVQTYSMVGLINAAIRLSMRWDQA 591


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: 957
Number of extensions: 53
Number of successful extensions: 7
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: 592
Length adjustment: 38
Effective length of query: 630
Effective length of database: 554
Effective search space:   349020
Effective search space used:   349020
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 Apr 09 2024. 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:

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