Alignments for a candidate for Dshi_1194 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Halomonas desiderata SP1

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_086508281.1 BZY95_RS01725 TRAP transporter permease DctM/Q

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_002151265.1:WP_086508281.1
          Length = 653

 Score =  386 bits (992), Expect = e-111
 Identities = 227/581 (39%), Positives = 338/581 (58%), Gaps = 23/581 (3%)

Query: 165 RERSVFSVP--DLVLIVCSLAVAAYFL-----VVYNTSMRMSTGTSFAPVGISFAAIAGT 217
           R+R    VP  D+V I   +AV+AY++     ++Y     M T          F  +A  
Sbjct: 73  RQRDAKRVPWYDIVPIALGVAVSAYYVHHFDRIIYQLGYLMPTTLDL------FFGVAAI 126

Query: 218 ALIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVY-TDAGILGP 276
            L++E  RR  G+A  I+ L+ LAY   G +LPG  G+ G       +  Y +  G+ G 
Sbjct: 127 LLLLEACRRAIGLAFPILVLIALAYAAFGNHLPGVWGHGGYRWDDLVATFYMSPTGVYGS 186

Query: 277 TTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGT 336
               SST I++FI+F A L ++  GD F+  + AA GR  GGPAK +   S + G I+G+
Sbjct: 187 LMRTSSTVIVIFIMFGALLVTTGGGDSFMRLSNAATGRMSGGPAKAATLCSAMFGSISGS 246

Query: 337 SAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYT 396
           +A NV +TG  TIPLMKK GYS + A A EA+ASTGGQI+PPIMGA AF+MA++    Y 
Sbjct: 247 TAANVATTGVFTIPLMKKNGYSPRFAAATEASASTGGQILPPIMGAAAFVMADVISTSYL 306

Query: 397 EIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQC-YLFVPIIILIV 455
            I  AA+IPA+L++ +++  V FEA + G+  + + E P LR  +     L +P+I+LI 
Sbjct: 307 NIISAALIPALLFYLAIWMSVHFEAKRLGLNPIPKSERPTLRQGLYNIETLVIPLIVLIT 366

Query: 456 ALFMGYSVIRAGTLATVSAAVV---SWLSPNKM--GLRHILQALEIASYMAIQIIVVCAA 510
            L M Y+   A   A  +A  +   SW SP      ++ +  ALE  +  A  I V+  +
Sbjct: 367 LLVMRYTPTTAAVAAYFTAMALYLFSWRSPGTFVERVKSLPAALEAGAMTAAMIAVIIGS 426

Query: 511 AGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVV 570
             +I  VISLTG+G + S ++L V+    L+ L+ AM ++I+LGMG+PT AAY +AASVV
Sbjct: 427 VAIIAAVISLTGLGLKVSSVILIVSGGDVLITLLLAMVVAIILGMGLPTVAAYMLAASVV 486

Query: 571 APGLVQLGIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAA 630
           A   ++ G+  L+AH F+ YFA++S +TPPVALA+Y    I+G++   T++ + +I +  
Sbjct: 487 AAAFIEAGLPSLSAHLFILYFAILSGVTPPVALAAYIGGAIAGSHWFRTALTATKISLGG 546

Query: 631 FIVPFMFFYNGALLMEAGWFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAA 690
           F++PFMF Y+  LL +    +IA A+ +   G+  L+   +G+F     SW+ R LL+AA
Sbjct: 547 FLIPFMFIYHPPLLGDGTGLQIALAVGSGVLGITALAASTIGYFLR-PCSWLERGLLLAA 605

Query: 691 ALLMIEGGLWTDLTGIAL--AVLAFVIQKQRKTRLATAGAL 729
           AL++I G L TD  GIAL  AV A+  +  R T  A++  L
Sbjct: 606 ALMLISGQLVTDALGIALIGAVWAWQYRLNRSTLGASSSPL 646


Lambda     K      H
   0.327    0.139    0.410 

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: 1215
Number of extensions: 67
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 729
Length of database: 653
Length adjustment: 39
Effective length of query: 690
Effective length of database: 614
Effective search space:   423660
Effective search space used:   423660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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)
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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