Alignments for a candidate for treEIIA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas stutzeri RCH2

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate GFF3291 Psest_3355 phosphoenolpyruvate-protein phosphotransferase

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



>FitnessBrowser__psRCH2:GFF3291
          Length = 960

 Score =  513 bits (1321), Expect = e-149
 Identities = 301/674 (44%), Positives = 408/674 (60%), Gaps = 23/674 (3%)

Query: 171 SKPVHLPNPNGLHARPAAVFAQAAKGFAASICLH---KQQDSANAKSLVAIMALQTVHGD 227
           S  V L N +GLHARPA V  + A+ F   I +     +    + KSL  ++A+    G 
Sbjct: 284 SAQVPLANAHGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQ 343

Query: 228 ALQVSAVGEDAELAISTLAQLLADGCGEAVTPVAVVA----PVVEAQEVSTKLL------ 277
            L+  A    A  A+  L + + +G GE V P+        P V AQ  +   +      
Sbjct: 344 LLEFMAEPAIASDALPALVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALR 403

Query: 278 -----RGVCASAGSAFGYVVQVAERTLEMPEFAADQQLERESLERALMHATQALQRLRDN 332
                 G+ AS G A G V+    + ++ P+      +E + L+ AL      +  L D 
Sbjct: 404 AGDQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDE 463

Query: 333 AAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLA 392
           +   +  DIF  HQ +L+DP+L E+ Q  + +G SA  AW    E+ A   ++L   LLA
Sbjct: 464 SQVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLA 523

Query: 393 ERALDLMDVGQRVLKLILGVPDGVWELPDQA-ILIAEQLTPSQTAALDTGKVLGFATVGG 451
           ERA DL DVG+RVL  + GV     + PD+  IL+ +++ PS  A L+  +V G  T GG
Sbjct: 524 ERAADLRDVGRRVLACLTGVE--AEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGG 581

Query: 452 GATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQ 511
           GATSH AI+ARALG+PA+ G    VL LA  T +LLD ++GEL + P+ + +EQ  ++R 
Sbjct: 582 GATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERA 641

Query: 512 QQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQR 571
            + +R     E    AAVTRDGH  E+ AN+ +  ET +A+++GAEGIGLLR+E ++   
Sbjct: 642 AREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNH 701

Query: 572 SVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLC 631
           S AP+   Q   Y  +  AL   R LVVRTLDVGGDKPL Y PM +E NPFLG+RGIRL 
Sbjct: 702 SQAPNQATQEAEYRRVLEAL-EGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLS 760

Query: 632 LERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPKLGI 691
           L+RP +L  Q RA+L+SA    L IM PMV  + E R A+ M++   + L + +L ++GI
Sbjct: 761 LQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADL-QVGI 819

Query: 692 MIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIAST 751
           MIE+P+AAL+A + A EVDFFSIGTNDLTQYTLA+DR HP L+ QAD  HP+VLRLI  T
Sbjct: 820 MIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMT 879

Query: 752 VKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAI 811
           V+AAHAHGKWVGVCG LA++ LAVPLL+GLGVDELSVS   I  +KA +RE++ + CQ +
Sbjct: 880 VEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRL 939

Query: 812 AHQVLGLESAEQVR 825
           A Q L L  A +VR
Sbjct: 940 AQQALMLPGAHEVR 953


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: 1781
Number of extensions: 86
Number of successful extensions: 6
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: 960
Length adjustment: 43
Effective length of query: 801
Effective length of database: 917
Effective search space:   734517
Effective search space used:   734517
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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Candidates (tab-delimited)
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 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