Alignments for a candidate for rbsK in Tatumella morbirosei LMG 23360

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Tatumella morbirosei LMG 23360

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_038017297.1 HA49_RS01050 ribokinase

Query= reanno::pseudo1_N1B4:Pf1N1B4_6031
         (305 letters)



>NCBI__GCF_000757425.2:WP_038017297.1
          Length = 402

 Score =  219 bits (559), Expect = 6e-62
 Identities = 126/292 (43%), Positives = 183/292 (62%), Gaps = 5/292 (1%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60
           M  KV ++GS N+D+V R  R P+GGE+L+ K  +   GGKGANQA+AA+  GA+V  V 
Sbjct: 97  MNGKVCILGSFNVDIVARVERFPKGGESLLAKGSSLGPGGKGANQALAASCAGAKVHFVS 156

Query: 61  CVGNDAYGEALRGALLAEQIDCQAV-STVEDSSGVALIVVDD-NSQNAIVIVAGANGALT 118
            VG+D + +     L A  I    +  + ++ +G A+I V + N +N I I  GAN  LT
Sbjct: 157 KVGSDQFSQFAFDHLTASDIHSLRLWQSEKEPTGNAIIYVSEANGENMIAIYPGANKTLT 216

Query: 119 PEVIDRFDAVLQAADVIICQLEVP-DATVGHALKRGRELGKTVILNPAPASRPLPVDWYA 177
            + I      L ++++++ QLE   DAT+ +A++  +EL   V+LNPAP S  + + W  
Sbjct: 217 SDEIADMAEELASSEILLVQLENNFDATL-NAIRLAKELSVRVVLNPAPVSEEI-ISWLP 274

Query: 178 AIDYLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEH 237
            +D L PNE+EASVLSG+ V  L +A+ AA ++ A+GA ++IIT+GS+G+L  DGQ+F+H
Sbjct: 275 MVDILTPNETEASVLSGIEVKDLESAKQAARKIAALGARQIIITMGSRGALLYDGQQFQH 334

Query: 238 FPAAKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGA 289
            P+    +VDTT AGD F G F AALAAG+ E  A  F    A+L+V R GA
Sbjct: 335 IPSFPALSVDTTGAGDAFNGAFVAALAAGESEVQAATFASAFASLAVEREGA 386


Lambda     K      H
   0.316    0.132    0.369 

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: 274
Number of extensions: 17
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: 305
Length of database: 402
Length adjustment: 29
Effective length of query: 276
Effective length of database: 373
Effective search space:   102948
Effective search space used:   102948
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: 49 (23.5 bits)

Align candidate WP_038017297.1 HA49_RS01050 (ribokinase)
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02152.hmm
# target sequence database:        /tmp/gapView.585990.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02152  [M=298]
Accession:   TIGR02152
Description: D_ribokin_bact: ribokinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      4e-97  311.1   0.8      5e-97  310.8   0.8    1.1  1  NCBI__GCF_000757425.2:WP_038017297.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000757425.2:WP_038017297.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.8   0.8     5e-97     5e-97       1     295 [.     101     394 ..     101     397 .. 0.98

  Alignments for each domain:
  == domain 1  score: 310.8 bits;  conditional E-value: 5e-97
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkk 73 
                                           ++++GS+nvD+v+rv+r+pk Ge++ a+  ++++GGKGANQA+aa+  ga+v++++kvG+D+f++ + ++l++
  NCBI__GCF_000757425.2:WP_038017297.1 101 VCILGSFNVDIVARVERFPKGGESLLAKGSSLGPGGKGANQALAASCAGAKVHFVSKVGSDQFSQFAFDHLTA 173
                                           79*********************************************************************** PP

                             TIGR02152  74 egidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletvee 145
                                           ++i+   + +++k++tG A+i v+e +geN I ++ Gan++lt++++++++e++++s+++l+QlE + +++ +
  NCBI__GCF_000757425.2:WP_038017297.1 174 SDIHSLRLWQSEKEPTGNAIIYVSEaNGENMIAIYPGANKTLTSDEIADMAEELASSEILLVQLENNFDATLN 246
                                           ***********************86479********************************************* PP

                             TIGR02152 146 alkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviit 218
                                           a+++ak+ +v v+lnPAP ++++  ++l +vdi++pNetEa++L+giev+dle+a++aa+k+ + g++++iit
  NCBI__GCF_000757425.2:WP_038017297.1 247 AIRLAKELSVRVVLNPAPVSEEI-ISWLPMVDILTPNETEASVLSGIEVKDLESAKQAARKIAALGARQIIIT 318
                                           *******************8877.9************************************************ PP

                             TIGR02152 219 lGskGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiP 291
                                           +Gs+Gall++ ++ ++ip++ +  vDtt+AGD+F+ga+++aLa+g+s  +a +fa+a+a+l+V r+Ga + +P
  NCBI__GCF_000757425.2:WP_038017297.1 319 MGSRGALLYDGQQFQHIPSFPALSVDTTGAGDAFNGAFVAALAAGESEVQAATFASAFASLAVEREGASN-MP 390
                                           ********************************************************************87.99 PP

                             TIGR02152 292 tkee 295
                                           ++e+
  NCBI__GCF_000757425.2:WP_038017297.1 391 SREQ 394
                                           9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (402 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.80
//
[ok]

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 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