Alignments for a candidate for rhaB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaB in Klebsiella michiganensis M5al

Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate BWI76_RS00680 BWI76_RS00680 rhamnulokinase

Query= reanno::Koxy:BWI76_RS00680
         (488 letters)



>FitnessBrowser__Koxy:BWI76_RS00680
          Length = 488

 Score =  989 bits (2556), Expect = 0.0
 Identities = 488/488 (100%), Positives = 488/488 (100%)

Query: 1   MSLRHCVAVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVDGFDCWDLDSLEGEI 60
           MSLRHCVAVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVDGFDCWDLDSLEGEI
Sbjct: 1   MSLRHCVAVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVDGFDCWDLDSLEGEI 60

Query: 61  RRGLEKVCEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQLGR 120
           RRGLEKVCEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQLGR
Sbjct: 61  RRGLEKVCEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQLGR 120

Query: 121 AEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTNAT 180
           AEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTNAT
Sbjct: 121 AEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTNAT 180

Query: 181 TTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGHWICPQGNHIPVVAVASHDTAS 240
           TTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGHWICPQGNHIPVVAVASHDTAS
Sbjct: 181 TTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGHWICPQGNHIPVVAVASHDTAS 240

Query: 241 AVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYRVLKNIMGL 300
           AVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYRVLKNIMGL
Sbjct: 241 AVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYRVLKNIMGL 300

Query: 301 WLLQRVLREQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAEIQAACRESGQPV 360
           WLLQRVLREQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAEIQAACRESGQPV
Sbjct: 301 WLLQRVLREQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAEIQAACRESGQPV 360

Query: 361 PDTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNELLNQLCADACGIT 420
           PDTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNELLNQLCADACGIT
Sbjct: 361 PDTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNELLNQLCADACGIT 420

Query: 421 VVAGPVEASTLGNIGIQLMTLDELNNVDEFRQVVRQNYALTTFTPNPENEIARFVAQFQP 480
           VVAGPVEASTLGNIGIQLMTLDELNNVDEFRQVVRQNYALTTFTPNPENEIARFVAQFQP
Sbjct: 421 VVAGPVEASTLGNIGIQLMTLDELNNVDEFRQVVRQNYALTTFTPNPENEIARFVAQFQP 480

Query: 481 QQNKELCA 488
           QQNKELCA
Sbjct: 481 QQNKELCA 488


Lambda     K      H
   0.320    0.135    0.413 

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: 978
Number of extensions: 33
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: 488
Length of database: 488
Length adjustment: 34
Effective length of query: 454
Effective length of database: 454
Effective search space:   206116
Effective search space used:   206116
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS00680 BWI76_RS00680 (rhamnulokinase)
to HMM TIGR02627 (rhaB: rhamnulokinase (EC 2.7.1.5))

# 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/TIGR02627.hmm
# target sequence database:        /tmp/gapView.32330.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02627  [M=454]
Accession:   TIGR02627
Description: rhamnulo_kin: rhamnulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.7e-237  773.1   0.0   4.4e-237  772.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00680  BWI76_RS00680 rhamnulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00680  BWI76_RS00680 rhamnulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  772.9   0.0  4.4e-237  4.4e-237       1     454 []       7     460 ..       7     460 .. 1.00

  Alignments for each domain:
  == domain 1  score: 772.9 bits;  conditional E-value: 4.4e-237
                               TIGR02627   1 vavdlGassGrvilaklenetkkltleeihrfknklvsqdgyevWdidaleqeillGlkkvkeeGialdsl 71 
                                             vavdlGassGrv+la+++ +++ l l+eihrf+n+l++ dg+++Wd+d+le ei+ Gl+kv+e+Gi +ds+
  lcl|FitnessBrowser__Koxy:BWI76_RS00680   7 VAVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVDGFDCWDLDSLEGEIRRGLEKVCEQGILIDSI 77 
                                             8********************************************************************** PP

                               TIGR02627  72 GidtWgvdyvlldkngervgdpvsyrdkrtdgvmakvqselgkeaiykktGiqflkfntlyqlkalkeenp 142
                                             GidtWgvdyvlldk+g+rvg pvsyrd+rt+g+m++++++lg+ +iy+++Giqfl+fntlyql+al e++p
  lcl|FitnessBrowser__Koxy:BWI76_RS00680  78 GIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQLGRAEIYRRSGIQFLPFNTLYQLRALVEQQP 148
                                             *********************************************************************** PP

                               TIGR02627 143 dllekvekllliPdylnyrltGklvaeytnasttqllnieekkwdkdlleylgvdaewfakitkpgsviGl 213
                                             +l+++++++lliPdy+++rltG++++eytna+ttql+ni++++wd+dll+++g+++ewf+++t+pg+viG+
  lcl|FitnessBrowser__Koxy:BWI76_RS00680 149 ELVSQAAHALLIPDYFSFRLTGNMNWEYTNATTTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGH 219
                                             *********************************************************************** PP

                               TIGR02627 214 leeldveevpvvavathdtasavvaaPledenaaylssGtWsliGlesetPitnekalkanitnegGadgr 284
                                             + +++++++pvvava+hdtasav+a+Pl ++naaylssGtWsl+G+es++P+t++ al+anitnegGa+gr
  lcl|FitnessBrowser__Koxy:BWI76_RS00680 220 WICPQGNHIPVVAVASHDTASAVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGR 290
                                             *********************************************************************** PP

                               TIGR02627 285 yrvlknimGlWllqrvarerdikdlaelieeakaepafkslinvnddrfinPenmveeikaycretnqavP 355
                                             yrvlknimGlWllqrv+re++++dl++li++++a pa++++i+ nddrfinP++m  ei+a+cre +q+vP
  lcl|FitnessBrowser__Koxy:BWI76_RS00680 291 YRVLKNIMGLWLLQRVLREQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAEIQAACRESGQPVP 361
                                             *********************************************************************** PP

                               TIGR02627 356 esaaelarcifdslallyrqvleelaelrgkdisklyivGGGsqnallnqliadlcgieviaGpveasalG 426
                                             +++aelarcifdslally +vl+ela lrg+++s+l+ivGGG+qn+llnql+ad+cgi+v+aGpveas+lG
  lcl|FitnessBrowser__Koxy:BWI76_RS00680 362 DTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNELLNQLCADACGITVVAGPVEASTLG 432
                                             *********************************************************************** PP

                               TIGR02627 427 nlgvqlialdeiedvaefrkivkksfel 454
                                             n+g+ql++lde+++v+efr++v++++ l
  lcl|FitnessBrowser__Koxy:BWI76_RS00680 433 NIGIQLMTLDELNNVDEFRQVVRQNYAL 460
                                             ************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (454 nodes)
Target sequences:                          1  (488 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.42
//
[ok]

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:

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