Alignments for a candidate for putP in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for putP in Pseudomonas putida KT2440

Align L-proline uptake porter, PutP (characterized)
to candidate PP_4946 PP_4946 sodium/L-proline transporter

Query= TCDB::Q9I5F5
         (506 letters)



>FitnessBrowser__Putida:PP_4946
          Length = 542

 Score =  801 bits (2068), Expect = 0.0
 Identities = 407/490 (83%), Positives = 443/490 (90%), Gaps = 2/490 (0%)

Query: 3   VNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWLLM 62
           +  P  ITFVIYIAAMVLIG AAYR+TNN SDYILGGRSLGS VTALSAGASDMSGWLLM
Sbjct: 51  MGNPLTITFVIYIAAMVLIGFAAYRATNNLSDYILGGRSLGSVVTALSAGASDMSGWLLM 110

Query: 63  GLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFEDNS 122
           GLPGA+Y +GLSE+WIAIGL VGAYLNWLFVAGRLRVQTEHNG+ALTLPDYF++RFEDNS
Sbjct: 111 GLPGAIYFAGLSEAWIAIGLTVGAYLNWLFVAGRLRVQTEHNGDALTLPDYFSSRFEDNS 170

Query: 123 RLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGFLA 182
            LLRI SA+VILVFFTIYCASGIVAGARLFESTFG+SYETALWAGAAATIAYTF+GGFLA
Sbjct: 171 GLLRIISAIVILVFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATIAYTFVGGFLA 230

Query: 183 VSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLKGASFIGVISLM 242
           VSWTDTVQASLMIFALILTPVIV+++TGG + TF AIE  +  +FDMLKGA+FIG+ISLM
Sbjct: 231 VSWTDTVQASLMIFALILTPVIVLISTGGFDQTFAAIEAVNPANFDMLKGATFIGIISLM 290

Query: 243 AWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAHPEQ 302
            WGLGYFGQPHILARFMAADSVKSI  ARRISMTWMILCL G  AVGFFGIAYF AHPE 
Sbjct: 291 GWGLGYFGQPHILARFMAADSVKSIAKARRISMTWMILCLAGTCAVGFFGIAYFSAHPEL 350

Query: 303 AGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKAFL 362
           AG VSEN ERVFIELAKILFNPW+AGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKAFL
Sbjct: 351 AGPVSENHERVFIELAKILFNPWVAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKAFL 410

Query: 363 RKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFSLLW 422
           RK ASQ+ELVWVGR MVL VA+IAI +A+NPENRVLGLV+YAWAGFGAAFGP+VL S+LW
Sbjct: 411 RKNASQVELVWVGRLMVLAVALIAIAMAANPENRVLGLVAYAWAGFGAAFGPVVLISVLW 470

Query: 423 KRMTRNGALAGMIVGAATVILWKNLLGWTGLYEIIPGFLFASVAIVVFSLLGKAPSTSML 482
           K MTRNGALAG++VGA TVILWKN     GLYEIIPGFLFAS+AIV+ S LG +PS +M+
Sbjct: 471 KGMTRNGALAGIVVGALTVILWKN-FDTLGLYEIIPGFLFASIAIVLVSKLG-SPSQTMV 528

Query: 483 KRFDDAEQEY 492
           KRF+ A+  Y
Sbjct: 529 KRFEAADAAY 538


Lambda     K      H
   0.326    0.138    0.421 

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: 1043
Number of extensions: 45
Number of successful extensions: 3
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: 506
Length of database: 542
Length adjustment: 35
Effective length of query: 471
Effective length of database: 507
Effective search space:   238797
Effective search space used:   238797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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)
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 2024 update 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