Alignments for a candidate for mglA in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Trichodesmium erythraeum IMS101

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_011610609.1 TERY_RS03785 D-ribose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_000014265.1:WP_011610609.1
          Length = 509

 Score =  600 bits (1547), Expect = e-176
 Identities = 299/501 (59%), Positives = 392/501 (78%), Gaps = 5/501 (0%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           +Y LEM+ I+K+F GV+AL    LKVRP ++H+L+GENGAGKSTL+KCLFGIY+ D+G I
Sbjct: 9   KYALEMTNISKTFSGVQALSGAILKVRPGTVHSLVGENGAGKSTLMKCLFGIYKLDAGEI 68

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET 130
              GK +   S ++AL  G+SMVHQELN V Q ++MDN+WLGRYP KG+F+D  K +++T
Sbjct: 69  YLSGKRVKIFSPQQALRYGVSMVHQELNQVRQMNIMDNIWLGRYPIKGIFIDTIKCFKDT 128

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
           K +F++L I+++P+  V +LS+S+MQ++EIAKA S N+KI++MDEPTSSLT  EV HLF+
Sbjct: 129 KNLFEKLSIELNPKRNVSSLSISEMQLVEIAKAVSSNSKIIVMDEPTSSLTVTEVEHLFS 188

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
           II +LK +  G++YISHK+EE+  + DE+T++RDG  IAT+P   LT  +II MMV R L
Sbjct: 189 IINQLKNQNVGVIYISHKIEEVLNISDEITIMRDGFCIATKPSQDLTKSEIIEMMVNRKL 248

Query: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
           +  FP K  + G+VILEV+NLT+  QPSI+D++F+L  GEILGIAGLVGAKRTDI+E +F
Sbjct: 249 SSLFPHKTCQLGKVILEVKNLTAYTQPSIKDINFELKAGEILGIAGLVGAKRTDILEGIF 308

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           GIR+ S+G I L GK+I+N   N+ I+ GFALVTEERRSTGI+  L + FN+ I+NI  Y
Sbjct: 309 GIRKVSSGEILLEGKKIDNSRINKVISQGFALVTEERRSTGIFDSLSVSFNATIANINYY 368

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
            N  GLL   +++  TQ +IDSM VKTP  +T IG LSGGNQQKVIIGRWLLT+P+ILML
Sbjct: 369 VNSWGLLSEKKIRQHTQEIIDSMGVKTPSQKTLIGKLSGGNQQKVIIGRWLLTKPKILML 428

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGIDVGAK+EIY+LI +LA +G GII++SSEM ELLG+TDRILVMSNG V+GIV++
Sbjct: 429 DEPTRGIDVGAKYEIYKLINDLANEGMGIIMVSSEMSELLGVTDRILVMSNGKVAGIVES 488

Query: 491 KTTTQN-----EILRLASLHL 506
           K  TQN     EI+ L+ L+L
Sbjct: 489 KKMTQNNRIQEEIMGLSGLYL 509


Lambda     K      H
   0.318    0.136    0.384 

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: 712
Number of extensions: 19
Number of successful extensions: 5
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: 506
Length of database: 509
Length adjustment: 34
Effective length of query: 472
Effective length of database: 475
Effective search space:   224200
Effective search space used:   224200
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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