GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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