Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E2

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf6N2E2_3339 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3339
          Length = 954

 Score =  510 bits (1313), Expect = e-148
 Identities = 308/670 (45%), Positives = 404/670 (60%), Gaps = 20/670 (2%)

Query: 171 SKPVHLPNPNGLHARPAAVFAQAAKGFAASICLH--KQQDSA-NAKSLVAIMALQTVHGD 227
           S  + L N +GLHARPA + AQ AK F   I +     QDSA +AKSL  +++L    G 
Sbjct: 284 SARIGLANAHGLHARPAKILAQLAKSFEGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQ 343

Query: 228 ALQVSAVGEDAELAISTLAQLLADGCGEAVTPV-----------AVVAPVVEAQEVSTKL 276
            L+  A    A  A+  L   + +G GE V P+           A VA V+ A E S  L
Sbjct: 344 VLEFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPE-SGSL 402

Query: 277 LRGVCASAGSAFGYVVQVAERTLEMPEFAADQQLERESLERALMHATQALQRLRDNAAGE 336
           ++ V A+ G A G       + ++ P       +ERE L+ AL    + +Q L + A  +
Sbjct: 403 IQAVAAAPGIAIGPAHIQVLQAIDYPLRGESAAIERERLQNALNQVRRDIQGLIERAKAK 462

Query: 337 AQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERAL 396
           A  +IF  HQE+L+DP L ++    +  G+SA  AW    EA A   ++L   LLAERA 
Sbjct: 463 AIREIFITHQEMLDDPELSDEVDTRLKLGESAQAAWMGVVEAAAKEQEALQDALLAERAA 522

Query: 397 DLMDVGQRVLKLILGVPDGVWELPDQA-ILIAEQLTPSQTAALDTGKVLGFATVGGGATS 455
           DL DVG+RVL  + GV       PDQ  IL+ +++ PS  A LD  +V G  T  GGAT+
Sbjct: 523 DLRDVGRRVLAQLCGVETP--NEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATA 580

Query: 456 HVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQ 515
           H AI+ARALG+PA+ G    VL LA GT +LLD  +G LH+DP  + +++   +R  + Q
Sbjct: 581 HSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTREQ 640

Query: 516 RHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAP 575
           R +   E     A+TRDGH  EV AN+   A    A+  GAEGIGLLR+E ++   S AP
Sbjct: 641 RLKVAAEQRHEPALTRDGHAVEVFANIGESAGVAGAVEQGAEGIGLLRTELIFMAHSQAP 700

Query: 576 SHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERP 635
               Q   Y  +   L   R LVVRTLDVGGDKPL Y P+  E NPFLG+RGIRL L+RP
Sbjct: 701 DEATQEAEYRKVLDGLAG-RPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRP 759

Query: 636 QLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEV 695
           Q++  Q RA+L SA    L IM PMV  + E R AR M E     + + +L +LGIMIEV
Sbjct: 760 QVMEAQLRALLRSADNRPLRIMFPMVGSVDEWRQARAMTERLRQEIPVADL-QLGIMIEV 818

Query: 696 PAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAA 755
           P+AAL+A + A EVDFFS+GTNDLTQYTLA+DR HP L++QAD  HP+VL+LI  TV+AA
Sbjct: 819 PSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAA 878

Query: 756 HAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQV 815
           HAHGKWVGVCG LA++ LAVP+L+GLGVDELSVS   I  +KA +RE+ L+  Q +A + 
Sbjct: 879 HAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQEA 938

Query: 816 LGLESAEQVR 825
           L + SA+ VR
Sbjct: 939 LAVGSADDVR 948


Lambda     K      H
   0.318    0.132    0.370 

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: 1716
Number of extensions: 87
Number of successful extensions: 5
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: 844
Length of database: 954
Length adjustment: 43
Effective length of query: 801
Effective length of database: 911
Effective search space:   729711
Effective search space used:   729711
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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