Alignments for a candidate for dhaK' in Tatumella morbirosei LMG 23360

GapMind for catabolism of small carbon sources

Alignments for a candidate for dhaK' in Tatumella morbirosei LMG 23360

Align glycerone kinase; EC 2.7.1.29 (characterized)
to candidate WP_038020213.1 HA49_RS02600 DAK2 domain-containing protein

Query= CharProtDB::CH_008528
         (552 letters)



>NCBI__GCF_000757425.2:WP_038020213.1
          Length = 546

 Score =  526 bits (1356), Expect = e-154
 Identities = 283/548 (51%), Positives = 367/548 (66%), Gaps = 6/548 (1%)

Query: 1   MSQFFFNQRTHLVSDVIDGAIIASPWNNLARLESDPAIRIVVRRDLNKNNVAVISGGGSG 60
           MS FF++ + +L+  VI+G I  SP  NL RL++D  +R+VVR D +K  VA++SGGGSG
Sbjct: 1   MSHFFYDSKENLIDLVIEGIIRTSPHANLTRLKTDSGLRVVVRNDWDKKQVALLSGGGSG 60

Query: 61  HEPAHVGFIGKGMLTAAVCGDVFASPSVDAVLTAIQAVTGEAGCLLIVKNYTGDRLNFGL 120
           HEP H GF+GKGMLT A+CGD+FASP VDAVL+AI  VTG+AGCLLIVKNYTGDRLNFGL
Sbjct: 61  HEPMHAGFVGKGMLTGAICGDIFASPGVDAVLSAIINVTGDAGCLLIVKNYTGDRLNFGL 120

Query: 121 AAEKARRLGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKIAGYFAERGYNLATVLREAQ 180
           AAEKAR LGY VE ++V DDI+LPDN  PRG++GTIL HKIAG+ A +G +L  V  + +
Sbjct: 121 AAEKARALGYKVETVLVEDDIALPDNPQPRGLSGTILAHKIAGFAASQGLSLQEVASQTR 180

Query: 181 YAASNTFSLGVALSSCHLP--QETDAAPRHHPGHAELGMGIHGEPGASVIDTQNSAQVVN 238
            A     +LGVALSSCHLP     D  P    G +ELGMGIHGE G + +DTQNS ++  
Sbjct: 181 SALKQIATLGVALSSCHLPGAGNNDRLP---AGKSELGMGIHGEHGVATLDTQNSREICE 237

Query: 239 LMVDKLLAALPETGRLAVMINNLGGVSVAEMAIITRELASSPLHSRIDWLIGPASLVTAL 298
            +  +LL  + +   L +MINNLGG SV E+A++++ L +SPL  R+  L GPA+LV+AL
Sbjct: 238 QITKRLLEHIGDKSDLLLMINNLGGFSVLELALLSQHLLASPLGKRVRLLQGPATLVSAL 297

Query: 299 DMKGFSLTAIVLEESIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALV 358
           DMKG SLT + L + +E+AL + V+ S W     P E+    +          PS N  +
Sbjct: 298 DMKGVSLTVLPLNDELEEALKSPVDVSGWSPLYSPAEMHWQQAQALPENTAVTPSDNPDI 357

Query: 359 AGIVELVTATLSDLETHLNALDAKVGDGDTGSTFAAAAREIASLLHRQQLPLNNLATLFA 418
           A ++E    TL D E  LN LD+ VGDGDTGST A  AR +   L  +QLPLN+ A L  
Sbjct: 358 AAMLESACQTLIDNEEALNTLDSHVGDGDTGSTLATGARYVLKALKDKQLPLNDPAALLG 417

Query: 419 LIGERLTVVMGGSSGVLMSIFFTAAGQKLEQGANVVEALNTGLAQMKFYGGADEGDRTMI 478
            +GE +T  MGGS GVL+S+ FTAA +  +   N  +A   GL QMK YGGA  GDRTMI
Sbjct: 418 WLGESITTPMGGSGGVLLSLLFTAAAEGYDPQQNPGKAFLKGLEQMKEYGGARPGDRTMI 477

Query: 479 DALQPALTSLLAQPKNLQAAFDAAQAGAERTCLSSKANAGRASYLSSESLLGNMDPGAQR 538
           DALQPA  ++ A          AA+ GAE T   SKA AGR++YL+++SL G++DPGA+ 
Sbjct: 478 DALQPAFEAMAAD-SGWDEVVAAARKGAESTAKMSKAGAGRSAYLNADSLQGHIDPGAKA 536

Query: 539 LAMVFKAL 546
           ++ VF A+
Sbjct: 537 VSEVFAAM 544


Lambda     K      H
   0.317    0.132    0.373 

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: 791
Number of extensions: 25
Number of successful extensions: 3
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: 552
Length of database: 546
Length adjustment: 36
Effective length of query: 516
Effective length of database: 510
Effective search space:   263160
Effective search space used:   263160
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: 53 (25.0 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 2024 update 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