Alignments for a candidate for treF in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Azospirillum brasilense Sp245

Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate AZOBR_RS09450 AZOBR_RS09450 alpha-amylase

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



>FitnessBrowser__azobra:AZOBR_RS09450
          Length = 1107

 Score =  247 bits (631), Expect = 1e-69
 Identities = 181/555 (32%), Positives = 264/555 (47%), Gaps = 113/555 (20%)

Query: 1   MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60
           +W+K+AVIYQ++ ++F D + DG+GD+ G+ ++L Y++ LGV  LWL PFY SP++D GY
Sbjct: 15  LWYKDAVIYQLHVKAFFDADNDGIGDIAGLTQKLDYIQELGVTTLWLLPFYPSPLRDDGY 74

Query: 61  DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESR-ASRNSPK 119
           D+ADY  V+P +G LQDF R L E H  GL+V+ +LV NHTS +HPWF  +R A   S  
Sbjct: 75  DIADYKAVNPSYGNLQDFKRFLRECHDRGLRVITELVINHTSDQHPWFQRARQAKPGSNH 134

Query: 120 RDWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAI 179
           R++Y+W D                   WT D     Y+ H+F   QPDLN+ NP+V + +
Sbjct: 135 RNFYVWSDTDQKYQGTRIIFCDTEKSNWTWDSEAQAYFWHRFYSHQPDLNFDNPKVLQEV 194

Query: 180 YEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETY 239
             VMRFWL  GVDG R+D +  L E    R+   N                  E+ PET+
Sbjct: 195 LNVMRFWLDMGVDGLRLDAVPYLKE----REGTNN------------------ENLPETH 232

Query: 240 AYVREMRQVLDEFSEPGRERVMVGEI------YLPYPQLVRYYQAGCHLPFNFHLIFR-- 291
             ++ +R  +D   +   +R+++ E        LPY   +      CH+ F+F L+ R  
Sbjct: 233 DVLKAIRTEID---KGYGDRMLLAEANQWPEDVLPYFGDLEKGGDECHMAFHFPLMPRIY 289

Query: 292 ---GLPDWRPENLARIVEEYESLLTRWDWPNWVLGNHDQ--------------------- 327
               + D  P  +A I+ +   +     W  + L NHD+                     
Sbjct: 290 MAVAMEDRHP--IADIMRQTPDIPDECQWAIF-LRNHDELTLEMVTDRERDYLWDFYAAD 346

Query: 328 ----------PRLASRLGEAQARVAAM--LLFTLRGTPTWYYGDEIGMKNGEIPPEKVQD 375
                      RLA  L   + ++  +  LL ++ GTP  YYGDEIGM            
Sbjct: 347 RRMRINLGIRRRLAPLLQNDRRKIELLKSLLLSMPGTPVLYYGDEIGM------------ 394

Query: 376 PAALRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEP---WLPVNPD----YKTRN 428
                     G++     RD  RTPMQW      GFS  +P   +LP   D    ++  N
Sbjct: 395 ----------GDNIYLGDRDGVRTPMQWSPDRNGGFSRADPARLYLPAIQDPIYGFQAIN 444

Query: 429 VAAQEQDPRSMLHLVRRLIALRKDPDLLYGAYR---TYRAREGVYAYLR-------GEGW 478
           V AQ++ P S+L+ ++RLIA+R+     +G  R    Y     V AYLR        E  
Sbjct: 445 VEAQQRSPSSLLNWMKRLIAVRQQ-HKAFGRGRFQLLYPGNRKVLAYLRCHSTEEGDEVI 503

Query: 479 LVALNLTEKEKALEL 493
           L   NL+   +A+EL
Sbjct: 504 LCVANLSRSAQAVEL 518


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: 1863
Number of extensions: 109
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: 1107
Length adjustment: 40
Effective length of query: 488
Effective length of database: 1067
Effective search space:   520696
Effective search space used:   520696
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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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