Aligments for a candidate for gtrB in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for gtrB in Magnetospirillum magneticum AMB-1

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate WP_011384964.1 AMB_RS13000 C4-dicarboxylate ABC transporter

Query= TCDB::P74224
         (445 letters)



>NCBI__GCF_000009985.1:WP_011384964.1
          Length = 486

 Score =  492 bits (1267), Expect = e-144
 Identities = 237/443 (53%), Positives = 331/443 (74%), Gaps = 13/443 (2%)

Query: 7   LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGT 66
           + P+MF   + FL  GYPVAF+L    I+F ++G  LG  +     A+P+RIFGIM N T
Sbjct: 9   MAPLMFAALVFFLLIGYPVAFALAANGIVFGLVGIELGLLNASLFQALPERIFGIMRNDT 68

Query: 67  LLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATV 126
           LLAIPFF F+G +LERSG+AE LL+T+G + G +RGGLA AVI VG +LAATTGVVAA+V
Sbjct: 69  LLAIPFFTFMGLILERSGMAEDLLDTIGQLFGPIRGGLAYAVIFVGALLAATTGVVAASV 128

Query: 127 VAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSL 186
           ++MGLISLPIMLRYGY + +ASGVI ASGTL QIIPPS+VLI++ADQLG SVGD++ G+ 
Sbjct: 129 ISMGLISLPIMLRYGYDRRVASGVIAASGTLAQIIPPSLVLIIMADQLGRSVGDMYAGAF 188

Query: 187 LPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLG 246
           +PG ++ G +A ++ ++  ++P  APALP E R++ G  L  R V  ++PPL+LI LVLG
Sbjct: 189 IPGFVLTGLYAGFIFLVTMIRPSFAPALPPEARSLRGMGLLLRTVTCLVPPLILIFLVLG 248

Query: 247 SIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFS 306
           +IF G+A+PTE GA+G+ GA+ LA   ++L+W  + +  D T +++  V+ IL+GST F 
Sbjct: 249 TIFIGVATPTEGGAMGAAGAMILALMKRKLDWNLMRQAMDTTAKLSCFVVFILVGSTVFG 308

Query: 307 LVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEA 366
           LVFRG+ GD ++  L+++LPGG++GFL ++ + +F+L FF+DFFE+AFI++PL  PVAE 
Sbjct: 309 LVFRGVNGDLWVEHLMSSLPGGKLGFLIVTNVLMFVLAFFLDFFELAFILVPLLGPVAEK 368

Query: 367 LNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPAS-------------LTTGQIYR 413
           + +DLIW+GV++G N+QTSF+ PPFGFALFYLR VAP +             +TTGQIY 
Sbjct: 369 MGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAPKTDYIDKITNKLTPKITTGQIYW 428

Query: 414 GAVPFIGLQVLVLLLIIIFPALI 436
           GAVPF+ +Q++++ L+I FP L+
Sbjct: 429 GAVPFVIIQIIMVGLVIAFPDLV 451


Lambda     K      H
   0.331    0.148    0.443 

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: 692
Number of extensions: 29
Number of successful extensions: 2
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: 445
Length of database: 486
Length adjustment: 33
Effective length of query: 412
Effective length of database: 453
Effective search space:   186636
Effective search space used:   186636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

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

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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, or view the source code.

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