Alignments for a candidate for treEIIA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Marinobacter adhaerens HP15

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components

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



>FitnessBrowser__Marino:GFF3781
          Length = 978

 Score =  484 bits (1246), Expect = e-140
 Identities = 303/709 (42%), Positives = 411/709 (57%), Gaps = 16/709 (2%)

Query: 131 EPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNPNGLHARPAAVF 190
           E   LL      +A  +P+  LS       ++ E  +A+ +K V L N +GLHARPA   
Sbjct: 272 ECHDLLERIDTFLAGDEPIQGLSAEALLARLSGEAADAVTAK-VTLLNTHGLHARPAKQL 330

Query: 191 AQAAKGFAASI---CLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELAISTLAQ 247
            Q A+   ASI    L  +  + +A SL  ++ L    G  L +SA G+DA  AI +L  
Sbjct: 331 VQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLLSATGDDASQAIQSLTS 390

Query: 248 LLADGCGEAVTPVAVVAP---VVEAQEVST----KLLRGVCASAGSAFGYVVQVAERTLE 300
            +  G GE V+P+    P   V EA++       + ++ V AS G A      + + TLE
Sbjct: 391 AIEGGLGEKVSPLRSADPQTKVPEAEQAPALTDDQPVKAVAASPGLALAPAFVMRQPTLE 450

Query: 301 MPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQA 360
            P+FA D + + + L +A+  A   L+ L   A G   A I   H E+L+D  L +    
Sbjct: 451 YPQFAEDSEQQIQRLNQAVDSADGQLRTLIRQAEGGEAAPILSVHVEMLQDEDLYQATLE 510

Query: 361 LIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELP 420
            I EG SA   W  A +  A   ++L   LLAERA DL DVG+RVL  + GV   +   P
Sbjct: 511 AINEGASAEAGWWKAIDTAARGQEALADRLLAERAADLRDVGRRVLSNLCGV--AMPTPP 568

Query: 421 DQA-ILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSL 479
           D   IL+A+ L PS  A LDT +V G  T  GGATSH AILARALGLPAV G   ++L++
Sbjct: 569 DTPYILVADDLGPSDVARLDTTRVRGLVTARGGATSHSAILARALGLPAVVGTGERILTI 628

Query: 480 ASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVT 539
            +G+ +++D ++G L  +P     E++  + QQ         EN  + A T DGH  EV 
Sbjct: 629 LNGSDLVVDGERGCLVPNPGAERCEKIRRRLQQLDALQAEAHENRNQPATTVDGHTIEVC 688

Query: 540 ANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVV 599
           AN+ + A T  A+  GA+G+GLLR+EF++     AP    Q   Y     AL     LV 
Sbjct: 689 ANLGNTAHTPDAVERGADGVGLLRTEFIFMAHPEAPDLATQVTEYQHAFDALNGLP-LVA 747

Query: 600 RTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLP 659
           RTLDVGGDKPL Y P+  E NPFLGMRGIRL L RP +L  Q RA+L++AG   L IM P
Sbjct: 748 RTLDVGGDKPLDYWPLPQEDNPFLGMRGIRLSLTRPDILETQVRALLTAAGDRPLRIMFP 807

Query: 660 MVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDL 719
           MV  L E R AR ++ +    +    + ++G+MIEVP+ AL+A   APEVDFFSIGTNDL
Sbjct: 808 MVKDLEEFRAARAIVTKVQSEVSASNV-QVGVMIEVPSCALLASTLAPEVDFFSIGTNDL 866

Query: 720 TQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLL 779
           TQYTLA+DR H +L++++D  HPSVLRLI  TV+AAHAH +WVGVCG LAS+  A+P+L+
Sbjct: 867 TQYTLAIDRGHGQLSAESDGLHPSVLRLIRMTVEAAHAHNRWVGVCGELASDPQAIPVLV 926

Query: 780 GLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREAL 828
           GL VDELSV+   +P +KA IR + L + +  A + L L +A +VR+AL
Sbjct: 927 GLDVDELSVTSRRVPLVKACIRGLNLENARQQAEKALSLATASEVRDAL 975


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: 1709
Number of extensions: 68
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: 978
Length adjustment: 43
Effective length of query: 801
Effective length of database: 935
Effective search space:   748935
Effective search space used:   748935
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