Aligments for a candidate for pgmA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for pgmA in Dinoroseobacter shibae DFL-12

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 3608627 Dshi_2020 phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I (RefSeq)

Query= BRENDA::Q9SCY0
         (623 letters)



>FitnessBrowser__Dino:3608627
          Length = 543

 Score =  577 bits (1487), Expect = e-169
 Identities = 289/550 (52%), Positives = 389/550 (70%), Gaps = 14/550 (2%)

Query: 74  TKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGRYFNKE 133
           T PI GQK GTSGLRK  + F   ++L N++QA++N +        TLVLGGDGRYFN E
Sbjct: 8   TAPIPGQKPGTSGLRKTTREFQAPHFLENYVQAIWNGIG--GVAGKTLVLGGDGRYFNAE 65

Query: 134 ASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPEYDWGI 193
           A+Q+++++AA +G  +++VG+  +LSTPA S +IRKR  +GG I+SASHNPGGPE D+G+
Sbjct: 66  AAQVVLRMAAASGAARVIVGQGALLSTPAASHLIRKRGTDGGIILSASHNPGGPEGDFGV 125

Query: 194 KFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVIDPVSDY 253
           K+N  +G PA E +TD+I+  T +I++  + +  D+DLS +G T+ G   VEV+DPV+DY
Sbjct: 126 KYNGPNGGPATEEVTDRIFAATQAITDYAMLDAQDVDLSTLGETRLGQMVVEVVDPVADY 185

Query: 254 LELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNGVPLED 313
             LM ++FDF+ IR LL+R  F   FDAMHA+TG YAK I  D LGA P S+ NG P  D
Sbjct: 186 AALMAEIFDFEAIRALLARG-FRLHFDAMHAITGPYAKAILEDTLGAAPGSVVNGTPSPD 244

Query: 314 FGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVAIIAAN 373
           FG GHPDPN  +AK+LVD M   + PDFGAASDGDGDRNM++G   +VTPSDS+A++AAN
Sbjct: 245 FGGGHPDPNPIWAKELVDRMMGPDAPDFGAASDGDGDRNMIMGRGIYVTPSDSLAVLAAN 304

Query: 374 AQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKLSICGE 433
           A   +P +  G  G+ARSMPTS ALDRVAE L +  +E PTGWKFFGNL+DAG+ ++CGE
Sbjct: 305 ATR-VPAYADGLAGVARSMPTSRALDRVAEALSIDCYETPTGWKFFGNLLDAGRATLCGE 363

Query: 434 ESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGRNFFSR 493
           ES GTGSDH+REKDG+WAVL WL+ILA         D   SVAD++ ++WA +GR+++SR
Sbjct: 364 ESAGTGSDHVREKDGLWAVLFWLNILA---------DSRASVADLMADHWARFGRHYYSR 414

Query: 494 YDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASKQGVRF 553
           +DYE  ++  A  +++ LR  L+        G  +  FAD+FSY DPVDGS ++ QG+R 
Sbjct: 415 HDYEAVDTAAAKGVMDALRARLADLPGTTAAGRQI-AFADEFSYDDPVDGSHSAGQGLRV 473

Query: 554 VFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVSKLKDF 613
            FTDG+R++ RLSGTG+ GAT+R+Y+E F P     D D Q AL P+I  A +++++   
Sbjct: 474 GFTDGARLVIRLSGTGTVGATLRVYLEAFVPGPEGLDRDPQEALAPMIAAAEALAEIATR 533

Query: 614 TGREKPTVIT 623
           TGR  P VIT
Sbjct: 534 TGRTAPDVIT 543


Lambda     K      H
   0.317    0.136    0.399 

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: 1002
Number of extensions: 50
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: 623
Length of database: 543
Length adjustment: 36
Effective length of query: 587
Effective length of database: 507
Effective search space:   297609
Effective search space used:   297609
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 (21.6 bits)
S2: 53 (25.0 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, 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