Alignments for a candidate for treEIIA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Shewanella sp. ANA-3

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 7025893 Shewana3_3042 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)

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



>FitnessBrowser__ANA3:7025893
          Length = 744

 Score =  291 bits (746), Expect = 7e-83
 Identities = 199/564 (35%), Positives = 299/564 (53%), Gaps = 17/564 (3%)

Query: 276 LLRGVCASAGSAFGYVVQVA-ERTLEMPEFAA-DQQLERESLERALMHATQALQRLR--- 330
           L +G  AS+G A  + + +  E +LE P+    D  LE   L  A+    +A+  L    
Sbjct: 169 LFQGTSASSGIAIAHALVLGGEISLEQPDVRCEDIVLESSRLVAAMGRCKEAIGALSQRF 228

Query: 331 DNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTL 390
           D    E  A IF A Q LL+D SL  +    + +G  A  A +  +      F ++    
Sbjct: 229 DREQDEEVASIFNALQLLLDDVSLGGEYAREVQQGWEAESAVSRVSLRYIQQFLAMEDPY 288

Query: 391 LAERALDLMDVGQRVLKLILGVPDGVWELPDQ-AILIAEQLTPSQTAALDTGKVLGFATV 449
           L ERA D+ D+GQ+VL+ ++  P+ +   PD+  IL+  +   +  A     K+ G  T 
Sbjct: 289 LKERASDIRDLGQKVLRQLIE-PERLELEPDKPVILVTREADATMLAEFPRQKLAGIVTE 347

Query: 450 GGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLL-DADKGELHLDPAVSVIEQLHA 508
            GG  SH AILARALG+PA+ G+  Q+LS     ++L+ +A +G+L + P+ +++ +  +
Sbjct: 348 LGGVNSHAAILARALGVPAITGVE-QLLSADIDQKLLVVNASRGQLMVSPSPAIVSEYRS 406

Query: 509 KRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLY 568
               Q+   +   +  A  +V  DG    +  N   L+     ++ GA+GIGL R+E  +
Sbjct: 407 LISAQKALQRQYAQELALPSVMLDGTRIRLYLNAGLLSGVASEIAEGADGIGLYRTEIPF 466

Query: 569 QQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGI 628
             +   PS  EQ   Y  +  A    R +V+RTLDVGGDKPL Y P+  E NPFLG RGI
Sbjct: 467 MLQQRFPSESEQVKVYQQVLSAASG-RPVVMRTLDVGGDKPLPYFPI-KEDNPFLGWRGI 524

Query: 629 RLCLERPQLLREQFRAILSSAGLAR-LHIMLPMVSQLSELRLARLMLEEEALAL-----G 682
           RL L+ P+L   Q RA+L + G  + L I+LPMVS L E+  +   LE+  + L      
Sbjct: 525 RLSLDHPELFLVQLRAMLQAGGECKQLSILLPMVSNLDEIDQSLAYLEQAYVELKNDVNS 584

Query: 683 LRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHP 742
             E+P++GIM+EVPA     D  A  VDF S+G+NDLTQY LA+DR++PR++S  DS+HP
Sbjct: 585 QIEMPRIGIMLEVPALLYQLDEVAKRVDFVSVGSNDLTQYLLAVDRNNPRVSSLFDSYHP 644

Query: 743 SVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIRE 802
            +LR +         H   + +CG LA E +   LL+ +G   LS++   +  I   +R 
Sbjct: 645 GILRALHQARLDCDYHELDISICGELAGEPMGAILLVAMGYQHLSMNQGSLARINYLLRR 704

Query: 803 VELSDCQAIAHQVLGLESAEQVRE 826
           V  +D   +  Q L L +  QVRE
Sbjct: 705 VSRADLTQLLSQALSLSNGFQVRE 728


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: 1160
Number of extensions: 53
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: 744
Length adjustment: 41
Effective length of query: 803
Effective length of database: 703
Effective search space:   564509
Effective search space used:   564509
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: 55 (25.8 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