Alignments for a candidate for PS417_11890 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Pseudomonas putida KT2440

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

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



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  346 bits (888), Expect = 1e-99
 Identities = 188/491 (38%), Positives = 285/491 (58%), Gaps = 2/491 (0%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86
           +LE+  + K F    AL    LRV  GSV  L+GENGAGKSTL+K++AGI++PDAG L L
Sbjct: 5   VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64

Query: 87  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146
            G+P    +P    + GI  IHQE  L    ++ E ++ G E+  G  ++D R   R  A
Sbjct: 65  DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFG-PLLDRRSQQREAA 123

Query: 147 QLL-ERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205
           +LL +   + L     +G LS AE+QMV+I +A+     +L+ DEP+ A+  +EV  L  
Sbjct: 124 RLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183

Query: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265
           I+  L+  G  I+YI+H + E+ ++ D V V R+G  +      +   + +  +MV RE+
Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREV 243

Query: 266 SQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325
            +L+P    P G LL+ VR L     ++G+   +  GEI+G+ GL+GSG   +  ++FG+
Sbjct: 244 GELYPKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGL 303

Query: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAG 385
            P D GE+ LDGQP+ +  P  A+ +G AL+ E+R+  G+   LSV EN  +A L  +  
Sbjct: 304 APPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFVR 363

Query: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445
            G +     R    ++ ++LR+K       +  LSGGNQQK  LA+W      + +LDEP
Sbjct: 364 LGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEP 423

Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505
           + GIDVGAK EIYRLI  L  EG  V+++SS+LPE++G+ DR+ VMH G +       EA
Sbjct: 424 SVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEA 483

Query: 506 TQERVMQLASG 516
             +R++ +A+G
Sbjct: 484 NSDRLLAVATG 494



 Score = 97.1 bits (240), Expect = 1e-24
 Identities = 66/241 (27%), Positives = 122/241 (50%), Gaps = 11/241 (4%)

Query: 35  KGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFD 94
           +G     A   + L+VR G ++ L G  G+G   L++ + G+  PD+GE+RL G+P++  
Sbjct: 262 RGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRLDGQPLSLR 321

Query: 95  TPLAALQAGIAMIHQELN---LMPHMSIAENIWIGREQLNGFHMID----HREMHRCTAQ 147
           +P  A+  G+A++ +E     +   +S+ EN  +    L+ F  +      RE H  T +
Sbjct: 322 SPREAVAQGVALMPEERRRQGVALDLSVQENTTLAA--LSRFVRLGLLSPARERHT-TLE 378

Query: 148 LLERLRINLD-PEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206
           L+ERLRI       +V  LS   +Q V +AK  +  S + ++DEP+  I       ++ +
Sbjct: 379 LIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPSVGIDVGAKVEIYRL 438

Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266
           I +L  +G G++ ++  + E+  + D + V   GA      A   + D L+++  G + +
Sbjct: 439 IGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEANSDRLLAVATGAQRA 498

Query: 267 Q 267
           Q
Sbjct: 499 Q 499



 Score = 82.4 bits (202), Expect = 4e-20
 Identities = 65/242 (26%), Positives = 105/242 (43%), Gaps = 14/242 (5%)

Query: 281 MSVRDLRLDGVFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGG 331
           MS   L L G+ K         G S  + AG + G+ G  G+G++ + + + GI   D G
Sbjct: 1   MSTPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAG 60

Query: 332 EICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQ 391
            + LDGQP     P      G   + ++R L   F     L                 Q+
Sbjct: 61  SLLLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQR 120

Query: 392 KALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDV 451
           +A R L  D    LR+   +L   I  LS   QQ   + R L+  PR+L+ DEP+  +  
Sbjct: 121 EAARLL--DDYFGLRLPANAL---IGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQ 175

Query: 452 GAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVM 511
                + R++  L  +G+A++ IS  L E+  + DRV V+  G  +  +     + E++ 
Sbjct: 176 REVERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQIT 235

Query: 512 QL 513
           +L
Sbjct: 236 RL 237


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: 614
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 521
Length of database: 512
Length adjustment: 35
Effective length of query: 486
Effective length of database: 477
Effective search space:   231822
Effective search space used:   231822
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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Candidates (tab-delimited)
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