Alignments for a candidate for treEIIA in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Oceanisphaera arctica V1-41

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_104485039.1 UN63_RS01625 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_002936955.1:WP_104485039.1
          Length = 949

 Score =  488 bits (1256), Expect = e-142
 Identities = 297/698 (42%), Positives = 408/698 (58%), Gaps = 27/698 (3%)

Query: 152 LSLGDPRTVVAQEEGEALFS-------------KPVHLPNPNGLHARPAAVFAQAAKGFA 198
           L+ G    +  Q+  EAL +             + V + N +GLHARP A+  QAAK F 
Sbjct: 252 LAAGRGAELAGQDSAEALLNVLKRGPVSLSSHQRTVVVRNTHGLHARPGAMLVQAAKNFD 311

Query: 199 ASI--C-LHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELAISTLAQLLADGCGE 255
           A I  C L   +   +AKSL+ ++ L    G  L   A G DAE A+  L + +  G GE
Sbjct: 312 ADIQVCNLDGDEHWVSAKSLMKMIGLGVKAGHQLVFRAEGPDAEAALDALTEAVNGGLGE 371

Query: 256 AVT-----PVAVVAPVVEAQEVSTK-LLRGVCASAGSAFGYVVQVAERTLEMPEFAADQQ 309
           A       P A    + E Q +    L+RGV AS G A G V   A    + P+ A D Q
Sbjct: 372 AFVAQATEPQAEEHDIHEPQGIDPNTLVRGVAASPGIAIGPVFVDAPLRFDYPQQAGDTQ 431

Query: 310 LERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAA 369
            E++ L  A+  A+  L       +     D+   H+ELL D SL +     I +G+SAA
Sbjct: 432 AEQQKLSAAIEQASAELSATLRRLSDTQARDMMSMHRELLADSSLTQGVSCRIKQGQSAA 491

Query: 370 FAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELPDQAIL-IAE 428
            AW S  ++ A    +    LLAERA D+ D+G+RV+ ++      +   P+   L +A+
Sbjct: 492 AAWWSEIDSAADRQAASSDALLAERAADIRDIGRRVMAILCH--SRMTPPPEHPYLWLAQ 549

Query: 429 QLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLD 488
            + PSQ   LD  +VLG  TVGGGA+SH AILAR+LG+PA+      V++L SGT  +L+
Sbjct: 550 DIGPSQLVNLDPSRVLGLVTVGGGASSHSAILARSLGIPALVAAGGAVMALPSGTEAILN 609

Query: 489 ADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAET 548
            D G L + P  +++EQ   ++Q++R++ + +      AA+T DGH   V AN+A   + 
Sbjct: 610 GDDGTLWVAPEAAMLEQARVRQQREREQAEQDWMRRHDAAITLDGHRIGVAANLADTGQA 669

Query: 549 EQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDK 608
            + M +GAEG+GLLR+EF++  R   P  DEQ   Y     AL   R LV RTLDVGGDK
Sbjct: 670 REVMEVGAEGVGLLRTEFVFMARHSEPDLDEQLAFYRQAFDALDG-RPLVARTLDVGGDK 728

Query: 609 PLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELR 668
           PL Y P+  E NPFLG+RGIRLC+++P+LL+ Q RA+L +AG   L IM PMV+  SE R
Sbjct: 729 PLPYWPVPKEDNPFLGVRGIRLCMQKPELLKTQLRALLMAAGDRPLRIMFPMVADWSEWR 788

Query: 669 LARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDR 728
            A+ + ++    +   ++ ++GIM+EVP+ AL A +FA EVDFFSIGTNDLTQYTLAMDR
Sbjct: 789 WAKALFDKIQSEVQATDV-QVGIMVEVPSVALNAAVFAEEVDFFSIGTNDLTQYTLAMDR 847

Query: 729 DHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSV 788
            +  LA  +D  +P+VLRLI   V AAHA GKWVGVCG LAS+ +A+PLLLGLGVDELSV
Sbjct: 848 GNGGLARLSDGLNPAVLRLIKMVVDAAHAKGKWVGVCGELASDPVALPLLLGLGVDELSV 907

Query: 789 SVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVRE 826
           S+  +  +KA +RE  LS C+ +A Q L    A  VR+
Sbjct: 908 SLKRVTLVKAQVREWSLSSCRKLAEQALQAVDAPAVRQ 945


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: 1584
Number of extensions: 60
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: 949
Length adjustment: 43
Effective length of query: 801
Effective length of database: 906
Effective search space:   725706
Effective search space used:   725706
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 24 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