Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens FW300-N2C3

Align Inositol transport system ATP-binding protein (characterized)
to candidate AO356_00965 AO356_00965 sugar ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00965
          Length = 517

 Score =  345 bits (886), Expect = 2e-99
 Identities = 184/475 (38%), Positives = 295/475 (62%), Gaps = 4/475 (0%)

Query: 39  LADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKA 98
           L D+ L +  G VLAL GENGAGKSTL KII G+  P  G+++ +G+     +   A++ 
Sbjct: 24  LTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEEL 83

Query: 99  GIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLARLRIN-LDPEEQ 157
           G+ M+ QELNL+P +S+AEN+++     +    ++ +++ +   E +A++ ++ +DP+  
Sbjct: 84  GVRMVMQELNLLPTLSVAENLFLDNLPSHG-GWISRKQLRKAAIEAMAQVGLDAIDPDTL 142

Query: 158 VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYIT 217
           VG L I  +QMVEIA+ +  D  +LI+DEPT+ +T +EV  LF  I  L+++G  I+YI+
Sbjct: 143 VGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYIS 202

Query: 218 HKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLL 277
           H++ E+  +A  +AV RDG+ + ++   + +S+ L+++MVGREL +   L    IG   L
Sbjct: 203 HRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRELGEHIDLGPRQIGAPAL 262

Query: 278 TVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKA-- 335
           TV+ LT     +DVSF++ +GEI GI+GL+G+GRT +   IFG  P+ SG + L   A  
Sbjct: 263 TVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTVALGSPARV 322

Query: 336 VRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCE 395
           V I  P  A+  G AL+TEDRK  GL    S+  N+ +  +P  +  G +   A  AL +
Sbjct: 323 VSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAGLVNGSAELALAQ 382

Query: 396 DMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYR 455
                +R+++ S  Q +  LSGGNQQK ++ RWL  +  +++ DEPTRGIDVGAK +IY 
Sbjct: 383 RQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVGAKFDIYA 442

Query: 456 LIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLA 510
           L+  L  +G A++++SS+L E++ + DR+ V+  G L+ T +R   TQ+ ++  A
Sbjct: 443 LLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAAA 497



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 62/226 (27%), Positives = 114/226 (50%), Gaps = 5/226 (2%)

Query: 287 VFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIE 346
           V  D++  L  GE+L + G  G+G++ +++ I G+   ++GQ+   G+  R      A E
Sbjct: 23  VLTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEE 82

Query: 347 KGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTP 406
            G  ++ ++  L    P LSV EN+ +  LP +   G+I +K LR    +   ++ +   
Sbjct: 83  LGVRMVMQELNL---LPTLSVAENLFLDNLPSH--GGWISRKQLRKAAIEAMAQVGLDAI 137

Query: 407 SLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMA 466
             +  +  L  G+QQ   +AR L+ +  +LILDEPT  +       ++  I  L + G+A
Sbjct: 138 DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVA 197

Query: 467 VIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
           +I IS  L E+  ++ R+ V+ +G L+     +    E+++ L  G
Sbjct: 198 IIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVG 243



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 65/232 (28%), Positives = 110/232 (47%), Gaps = 9/232 (3%)

Query: 31  KGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKP---I 87
           KG      + DV   VR G +  + G  GAG++ L+++I G    D+G + L G P   +
Sbjct: 265 KGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTVAL-GSPARVV 323

Query: 88  VFETPLAAQKAGIAMIHQEL---NLMPHMSIAENIWIGR-EQLNSLHMVNHREMHRCTAE 143
              +P  A   GIA+I ++     L+   SIA NI +G   +++S  +VN          
Sbjct: 324 SIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAGLVNGSAELALAQR 383

Query: 144 LLARLRI-NLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            +  +RI +  P + V  LS   +Q V I + +  D  +++ DEPT  I       ++++
Sbjct: 384 QVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVGAKFDIYAL 443

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLIS 254
           + +L  QGK +V ++  + E+  I D + V   G  I     DS   D L++
Sbjct: 444 LGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLA 495


Lambda     K      H
   0.320    0.136    0.381 

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: 581
Number of extensions: 27
Number of successful extensions: 8
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: 517
Length of database: 517
Length adjustment: 35
Effective length of query: 482
Effective length of database: 482
Effective search space:   232324
Effective search space used:   232324
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