Alignments for a candidate for treEIIA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Cupriavidus basilensis 4G11

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate RR42_RS01795 RR42_RS01795 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>FitnessBrowser__Cup4G11:RR42_RS01795
          Length = 591

 Score =  252 bits (644), Expect = 4e-71
 Identities = 181/590 (30%), Positives = 285/590 (48%), Gaps = 40/590 (6%)

Query: 277 LRGVCASAGSAFGYVVQVAERTLEMPEFAADQ-----QLERESLERALMHATQA-LQRLR 330
           L G+  S G A G    +A   L++  +  D+     ++ER    RA + A    L+R  
Sbjct: 5   LHGIPVSRGVAIGRAHLLAPAALDVSHYLVDEDRLDAEVERLRSARAAVRAELVTLKRDL 64

Query: 331 DNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKSLGST 389
              A E        H  +L+D +L  + +ALI   + +A +A  +  E     F  +   
Sbjct: 65  PREAPEELGAFLDVHAMILDDEALAREPEALIRNRRYNAEWALTTRLEELMRQFDEIEDE 124

Query: 390 LLAERALDLMDVGQRVLKLILGV--------------PDGVWELPDQAILIAEQLTPSQT 435
            L ER  D+  V +R+LK++ G               PDG  E     I++A  ++P+  
Sbjct: 125 YLRERKADIRQVVERILKVLAGAAVLAPAPVPPSSLAPDG--EPAPGVIVVAHDISPADM 182

Query: 436 AALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELH 495
                    GF T  GG TSH AI+AR+L +PA  G+      +     V++D D G + 
Sbjct: 183 LQFRHTVFHGFVTDLGGRTSHTAIVARSLDIPAAVGVQSASELIRQDDWVIIDGDAGLVI 242

Query: 496 LDPAVSVIEQLHAKRQQQRQRHQHELENAARA-AVTRDGHHFEVTANVASLAETEQAMSL 554
           +DP+  ++E+ +  RQ +R   +  L+      AVT DG   ++ AN+    +   A++ 
Sbjct: 243 VDPSAIILEE-YRHRQSERALEKKRLQRLRHTPAVTLDGLEIDLLANIEMAEDATAALTA 301

Query: 555 GAEGIGLLRSEFLYQ-QRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPL--- 610
           GA G+GL RSEFL+  +R   P  +EQ   Y     A+     + +RT+D+G DKPL   
Sbjct: 302 GAVGVGLFRSEFLFMNRRGELPDEEEQFEAYRGAVDAMHGLP-VTIRTIDIGADKPLDGR 360

Query: 611 -----AYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLS 665
                     ++  NP LG+R IR  L  P +   Q RA+L ++    + +++PM++   
Sbjct: 361 DGRDGRGDDFETALNPALGLRAIRWSLSEPAMFLTQLRALLRASAFGPVRLLIPMLAHAR 420

Query: 666 ELR-----LARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLT 720
           E+      +A+   + +A         K+G MIE+PAA LM  LF   +DF SIGTNDL 
Sbjct: 421 EIDQTLDLIAQAKRQLDARGQAFDPNIKVGAMIEIPAAVLMLPLFLRRMDFLSIGTNDLI 480

Query: 721 QYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLG 780
           QYTLA+DR    +A   D  HP+VL+LIA T++ A+  G  V VCG +A +     LLLG
Sbjct: 481 QYTLAIDRADNAVAHLYDPLHPAVLQLIARTIREANRAGVPVAVCGEMAGDPAMTRLLLG 540

Query: 781 LGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSV 830
           +G+ E S+    +  +K  +   +    + +  QVL     E++  AL +
Sbjct: 541 MGLREFSMHPSQLLRVKQEVLHADCERLERLVEQVLSAYEPEELACALKL 590


Lambda     K      H
   0.318    0.132    0.370 

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: 1056
Number of extensions: 52
Number of successful extensions: 5
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: 844
Length of database: 591
Length adjustment: 39
Effective length of query: 805
Effective length of database: 552
Effective search space:   444360
Effective search space used:   444360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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