Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens FW300-N1B4

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243
          Length = 521

 Score =  263 bits (671), Expect = 2e-74
 Identities = 167/491 (34%), Positives = 261/491 (53%), Gaps = 17/491 (3%)

Query: 18  NAIPV-DEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGI 76
           N +P+ D+   L++  +SK +PG +A   + L + PG + AL+GENGAGKSTLMKII G+
Sbjct: 3   NPVPIPDQIPRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGV 62

Query: 77  YQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMI 136
              D+GE+  +G+ VT   P  A   GI M+ Q  +L   +S+A+NI +      G    
Sbjct: 63  THADSGEMIWQGQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAG---- 118

Query: 137 DHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAIT 196
             +++     ++ +R  + L+PE  V +LSI ERQ VEI + +  D  +LI+DEPTS +T
Sbjct: 119 TPKQLEPKIREVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLT 178

Query: 197 DKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSL 256
            +E   LF  +  L A+G  I++I+HK+ EV ++     V R G   G           L
Sbjct: 179 PQEADELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQL 238

Query: 257 ISMMVGRELSQLFPVREKPIG-DLLMSVRDLRLDG------VFKGVSFDLHAGEILGIAG 309
             +MVG E ++L     K +G D  +SV  L            K + FD+ +GEI+G+AG
Sbjct: 239 AQLMVG-EAAELITDYPKVMGADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAG 297

Query: 310 LMGSGRTNVAEAIFG---ITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLF 366
           + G+G+  +   + G   +   D   I   GQPV    P    + G A +  +R   G  
Sbjct: 298 VAGNGQDELLALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAV 357

Query: 367 PCLSVLENMEMAVLPH-YAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQ 425
           P LS+ +N  +         +G +Q+  ++AL ED+ ++  VKTP       +LSGGN Q
Sbjct: 358 PELSLADNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQ 417

Query: 426 KALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMS 485
           K +L R ++  P++L+   PT G+DVGA A I+R +  L   G A+++IS +L E+  + 
Sbjct: 418 KFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQIC 477

Query: 486 DRVMVMHEGDL 496
           DR+  +  G L
Sbjct: 478 DRLGALCGGQL 488



 Score = 86.3 bits (212), Expect = 3e-21
 Identities = 65/248 (26%), Positives = 121/248 (48%), Gaps = 15/248 (6%)

Query: 275 PIGDLLMSVRDLRLDGVFKG------VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPS 328
           PI D +  ++  R+   + G      +   +  GEI  + G  G+G++ + + I+G+T +
Sbjct: 6   PIPDQIPRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHA 65

Query: 329 DGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGF 388
           D GE+   GQ V + +P  A   G  ++ +      LF  LSV +N+ +A+     G   
Sbjct: 66  DSGEMIWQGQRVTMRNPAQARGLGIGMVFQH---FSLFETLSVAQNIALAM-----GAAA 117

Query: 389 IQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRG 448
              K L     ++ ++  +     E+ + +LS G +Q+  + R LM + R+LILDEPT  
Sbjct: 118 GTPKQLEPKIREVSQRYGMALEP-ERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSV 176

Query: 449 IDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQE 508
           +      E++  +  LA+EG +++ IS +L EV  +     V+  G + G    ++ +  
Sbjct: 177 LTPQEADELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDR 236

Query: 509 RVMQLASG 516
           ++ QL  G
Sbjct: 237 QLAQLMVG 244



 Score = 54.7 bits (130), Expect = 8e-12
 Identities = 44/214 (20%), Positives = 91/214 (42%), Gaps = 9/214 (4%)

Query: 42  ALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAG---IYQPDAGELRLRGKPVTFDTPLA 98
           +L ++   VR G ++ + G  G G+  L+ +++G   + + D+  +   G+PV    P A
Sbjct: 279 SLKNIDFDVRSGEIVGVAGVAGNGQDELLALLSGEERLPRDDSATISFGGQPVAHLRPDA 338

Query: 99  ALQAGIAMIHQEL---NLMPHMSIAENIWIGREQ--LNGFHMIDHREMHRCTAQLLERLR 153
             + G+A +  E      +P +S+A+N  +   Q  L    ++   ++      ++ R  
Sbjct: 339 RRKLGLAFVPAERLGHGAVPELSLADNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRFG 398

Query: 154 INL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKA 212
           +   D      +LS    Q   + + +     +L+   PT  +     A +   +  L+ 
Sbjct: 399 VKTPDSLAPARSLSGGNLQKFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIALRD 458

Query: 213 QGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQ 246
            G  I+ I+  ++E+F I D +     G    LQ
Sbjct: 459 AGAAILVISEDLDELFQICDRLGALCGGQLSPLQ 492


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: 607
Number of extensions: 29
Number of successful extensions: 7
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: 521
Length adjustment: 35
Effective length of query: 486
Effective length of database: 486
Effective search space:   236196
Effective search space used:   236196
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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Protein sequences (fasta format)
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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