GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Herbaspirillum seropedicae SmR1

Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate HSERO_RS11645 HSERO_RS11645 alpha-amylase

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



>FitnessBrowser__HerbieS:HSERO_RS11645
          Length = 1121

 Score =  237 bits (604), Expect = 2e-66
 Identities = 174/551 (31%), Positives = 254/551 (46%), Gaps = 106/551 (19%)

Query: 1   MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60
           +W+K+AVIYQ++ +S+ D N DG+GD  G+ ++L Y+  LGV+ +WL PFY SP +D GY
Sbjct: 8   LWYKDAVIYQIHVKSYFDANDDGIGDFAGLIQKLDYITGLGVNTIWLLPFYPSPRRDDGY 67

Query: 61  DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASR-NSPK 119
           D+++Y +V P +G + D  R +  AH  GL+V+ +LV NHTS +HPWF  +R +R  S  
Sbjct: 68  DISEYKNVHPDYGNMSDVRRFIAAAHEHGLRVITELVINHTSDQHPWFQRARRARPGSVA 127

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

Query: 180 YEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETY 239
             VM FWL  G+DG R+D +  L E    R+   N                  E+ PET+
Sbjct: 188 LNVMSFWLDLGIDGLRLDAVPYLIE----REGTSN------------------ENLPETH 225

Query: 240 AYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYY---QAGCHLPFNFHL-------- 288
           A ++ +R  +D       +R+++ E  + +P+ V+ Y      CH+ F+F L        
Sbjct: 226 AILKRIRAEMD---SKYPDRMLLAEANM-WPEDVQQYFGDSDECHMAFHFPLMPRMYMAL 281

Query: 289 ----------IFRGLPDWRPE-NLARIVEEYESLLTRW--DWPNWVLGNHDQPRLASRLG 335
                     I R  PD   +   A  +  ++ L      D     L NH  P   +R+ 
Sbjct: 282 ASQDRFPITDILRQTPDIPADCQWAIFLRNHDELTLEMVTDAERDYLWNHYAPDRRARIN 341

Query: 336 EAQARVAAML--------------LFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAALRQ 381
               R  A L              L ++ GTP  YYGDEIGM                  
Sbjct: 342 LGIRRRLAPLVERDWRRIQLLNSFLLSMPGTPVIYYGDEIGM------------------ 383

Query: 382 KDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEPWLPVNP-------DYKTRNVAAQEQ 434
               G++     RD  RTPMQW      GFS V+P   V P        Y+T NV AQ  
Sbjct: 384 ----GDNIHLGDRDGVRTPMQWTPDRNGGFSRVDPARLVLPLLMDPQYGYQTINVEAQSA 439

Query: 435 DPRSMLHLVRRLIALRKDPDLL--YGAYRTYRAREGVYAYLR----------GEGWLVAL 482
           D  SML+ +RRL+ +RK             Y +   ++AYLR           E  L   
Sbjct: 440 DRHSMLNWMRRLLNVRKQHQAFGRGSLALVYPSNRKIFAYLREFTDPRPGGATETILCVA 499

Query: 483 NLTEKEKALEL 493
           N+++  +A+EL
Sbjct: 500 NVSQSAQAVEL 510


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: 1802
Number of extensions: 101
Number of successful extensions: 6
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: 1121
Length adjustment: 41
Effective length of query: 487
Effective length of database: 1080
Effective search space:   525960
Effective search space used:   525960
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 17 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