Alignments for a candidate for PS417_11890 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Cupriavidus basilensis 4G11

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  285 bits (728), Expect = 4e-81
 Identities = 175/490 (35%), Positives = 270/490 (55%), Gaps = 22/490 (4%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86
           +L +  ++K F  +VA  D+ L ++ G VLAL+GENGAGKSTL+ I+ G Y  DAG + +
Sbjct: 5   ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64

Query: 87  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146
            G+P+    P AAL AGI M+HQ   L  ++S+ +NI +G + L  + +  H    +  A
Sbjct: 65  DGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLA 124

Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206
            L ER  + + P+ +VG LS+ ERQ VEI KA+   + +LI+DEPT+ +T  E   LFS 
Sbjct: 125 -LAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFST 183

Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266
           +A L A+G  +I+I+HK++EV  ++D +AV R G  + L  A       L  +MVGR ++
Sbjct: 184 LAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVA 243

Query: 267 QLFPVREKPIGDLL-------------MSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGS 313
               V  +   D               +  R      + + VS  + AGEI+GIAG+ G+
Sbjct: 244 MPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSGN 303

Query: 314 GRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 373
           G+  +AE   G+  +  G I L G+P+  + P   I  G A + EDR   G+   L+V E
Sbjct: 304 GQAALAELASGMLEASEGRITLAGKPMS-AKPRAWIGAGVARVPEDRHAIGVVGDLAVWE 362

Query: 374 N--MEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLAR 431
           N   E    P ++  G I++ A +    D+  +  V+T  ++    T+SGGN QK +L R
Sbjct: 363 NAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILGR 422

Query: 432 WLMTN-----PRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSD 486
            L        PR+++  +PT G+D+GA A +   +   A EG AV++IS +L E+  ++D
Sbjct: 423 ALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALAD 482

Query: 487 RVMVMHEGDL 496
           R+ VMH G L
Sbjct: 483 RIAVMHAGHL 492



 Score = 99.4 bits (246), Expect = 3e-25
 Identities = 70/245 (28%), Positives = 122/245 (49%), Gaps = 19/245 (7%)

Query: 286 LRLDGVFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLD 336
           LRL G+ K          +S +L  GE+L + G  G+G++ +   +FG   +D G + +D
Sbjct: 6   LRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVD 65

Query: 337 GQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP--HYAGNGFIQQKAL 394
           GQP+    P  A+  G  ++ +   L+     LSVL+N+ +   P   +  +G   +  +
Sbjct: 66  GQPLPPGQPRAALTAGIGMVHQHFTLADN---LSVLDNIMLGTQPLWQWRLDGHAARGKV 122

Query: 395 RALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAK 454
            AL E     +R +       +  LS G +Q+  + + L    R+LILDEPT  +     
Sbjct: 123 LALAERFGLAVRPQAR-----VGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEA 177

Query: 455 AEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLA 514
             ++  ++ L +EG++VI IS +L EVL +SDR+ V+  G L+     ++ T+  + +L 
Sbjct: 178 ETLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELM 237

Query: 515 SGMSV 519
            G  V
Sbjct: 238 VGRVV 242


Lambda     K      H
   0.321    0.137    0.391 

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: 665
Number of extensions: 32
Number of successful extensions: 8
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: 521
Length of database: 530
Length adjustment: 35
Effective length of query: 486
Effective length of database: 495
Effective search space:   240570
Effective search space used:   240570
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: 52 (24.6 bits)

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

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