GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpB in Klebsiella michiganensis M5al

Align anaerobic glycerol-3-phosphate dehydrogenase subunit B (EC 1.1.5.3) (characterized)
to candidate BWI76_RS19970 BWI76_RS19970 anaerobic glycerol-3-phosphate dehydrogenase subunit B

Query= ecocyc::ANGLYC3PDEHYDROGSUBUNITB-MONOMER
         (419 letters)



>FitnessBrowser__Koxy:BWI76_RS19970
          Length = 419

 Score =  545 bits (1403), Expect = e-159
 Identities = 267/418 (63%), Positives = 319/418 (76%)

Query: 1   MRFDTVIMGGGLAGLLCGLQLQKHGLRCAIVTRGQSALHFSSGSLDLLSHLPDGQPVTDI 60
           M+FD  I+GGGLAGLLCGL L + GLR  I++RGQSALHFSS SLDLLS LP+G+ VTD+
Sbjct: 1   MKFDCAIIGGGLAGLLCGLALNQRGLRSVIISRGQSALHFSSASLDLLSTLPNGETVTDV 60

Query: 61  HSGLESLRQQAPAHPYSLLEPQRVLDLACQAQALIAESGAQLQGSVELAHQRVTPLGTLR 120
             G+  L +Q   HPY+ L  +RV+  A QAQAL A+ G  +QG     H RVTPLGTLR
Sbjct: 61  AHGIGQLARQLSEHPYARLGAERVMGYASQAQALFADCGIAMQGEASQPHLRVTPLGTLR 120

Query: 121 STWLSSPEVPVWPLPAKKICVVGISGLMDFQAHLAAASLRELGLAVETAEIELPELDVLR 180
           + WLS  E+   PLPA  +CVVGISG  DFQ HLAAASL + G+  E  EI+LP LDVLR
Sbjct: 121 AAWLSPQEIATAPLPANGVCVVGISGFGDFQPHLAAASLNQHGVHAEAQEIDLPLLDVLR 180

Query: 181 NNATEFRAVNIARFLDNEENWPLLLDALIPVANTCEMILMPACFGLADDKLWRWLNEKLP 240
           ++ +EFRA NIAR LD+E  WP LL AL P+A     I+MPACFGLADD+L++WL ++LP
Sbjct: 181 DSPSEFRAANIARRLDDETQWPALLAALRPLAQRHRFIIMPACFGLADDRLYQWLQQRLP 240

Query: 241 CSLMLLPTLPPSVLGIRLQNQLQRQFVRQGGVWMPGDEVKKVTCKNGVVNEIWTRNHADI 300
           C L LLPTLPPSV G+RL  QLQR F+R GG W+ GDEV  ++ +NG+VN IWTRNH DI
Sbjct: 241 CPLRLLPTLPPSVPGMRLHAQLQRHFIRGGGTWLTGDEVINISQQNGIVNAIWTRNHGDI 300

Query: 301 PLRPRFAVLASGSFFSGGLVAERNGIREPILGLDVLQTATRGEWYKGDFFAPQPWQQFGV 360
           PLRPRFAVLASGSFFS GLVAER+G+REPILGLD+ QT  R  WY+ DFFA QPWQ+FG+
Sbjct: 301 PLRPRFAVLASGSFFSNGLVAERSGVREPILGLDLQQTLPRERWYQQDFFASQPWQRFGL 360

Query: 361 TTDETLRPSQAGQTIENLFAIGSVLGGFDPIAQGCGGGVCAVSALHAAQQIAQRAGGQ 418
            TD  LRP   GQT+ENLFA+GS+LGGFD IA GCGGGVCAV+ALHAA+ I + AGG+
Sbjct: 361 KTDAALRPQLQGQTLENLFAVGSILGGFDAIALGCGGGVCAVTALHAARLIGELAGGE 418


Lambda     K      H
   0.321    0.137    0.426 

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: 591
Number of extensions: 16
Number of successful extensions: 1
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: 419
Length of database: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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