Aligments for a candidate for araB in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for araB in Shewanella sp. ANA-3

Align Ribulokinase (EC 2.7.1.16) (characterized)
to candidate 7024890 Shewana3_2064 ribulokinase (RefSeq)

Query= reanno::Cola:Echvi_0515
         (562 letters)



>FitnessBrowser__ANA3:7024890
          Length = 557

 Score =  607 bits (1564), Expect = e-178
 Identities = 298/550 (54%), Positives = 387/550 (70%), Gaps = 3/550 (0%)

Query: 5   FVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHLEGLE 64
           + +GLDYGSDSVRA++V+T  G    ++V +YPRWK G +C+P  NQFRQHPLD++E L 
Sbjct: 8   YALGLDYGSDSVRALLVDTQTGAEVATNVVYYPRWKKGLFCEPAKNQFRQHPLDYIESLI 67

Query: 65  ETIREV-IKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLWKDH 123
           E ++ +  K     A ++ G+ VDTTGS+P+AVD+ G  LAL PEF  NPNAM +LWKDH
Sbjct: 68  EVVQGLWAKAPSGAAQRVCGLSVDTTGSTPIAVDESGVALALKPEFENNPNAMFLLWKDH 127

Query: 124 TAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWMEHCD 183
           +AI EA +I   A     E+Y KYEGGIYSSEWFWAK L V+R D  V QAAYSW+EHCD
Sbjct: 128 SAIIEAKQITAAAND-SSENYLKYEGGIYSSEWFWAKALFVLRHDAEVRQAAYSWVEHCD 186

Query: 184 VITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYTETF 243
            ITA + G  +P   K  RCAAGHK +WHESW+G PP +F   +DP L  LRD+L  ET 
Sbjct: 187 WITALMTGTSHPKVFKAGRCAAGHKVMWHESWNGYPPNDFFVGIDPLLDGLRDKLPLETC 246

Query: 244 TSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDIMVA 303
           TSD   G L+ EWA+ LGLST+ +++ G+FD HAGAVG  V    L KVMGTSTCDI VA
Sbjct: 247 TSDKVCGQLTPEWAQHLGLSTEVIVSFGSFDCHAGAVGANVKPGVLTKVMGTSTCDITVA 306

Query: 304 THEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRASNVL 363
           ++E IG+  +KGICGQVDGSV+PG +GLEAGQS FGD+ AWF+ L   P   L   S + 
Sbjct: 307 SYEDIGERCIKGICGQVDGSVLPGMIGLEAGQSAFGDLYAWFRDLTAWPMQQL-DTSVLF 365

Query: 364 DEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVMGLN 423
           DE  K  LI +++S+ L  L   A +IP+ ET  VALDW+NGRRTPDA+Q++  A+ GL 
Sbjct: 366 DENIKAKLIQQLESETLTMLGNAAAKIPVGETGIVALDWINGRRTPDADQSVAMAITGLT 425

Query: 424 MGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADVLNM 483
           MG+ A +VFKALVE+  +G++ I++RF++EGV ID V+ +GG++KKS  +MQT ADV N 
Sbjct: 426 MGSQAPQVFKALVEASAYGARAIIERFKQEGVCIDHVVTIGGISKKSDFIMQTCADVWNC 485

Query: 484 PIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKALYAK 543
            I +  S+Q+ ALGAA+YA+ AAG++P   +A AAM +   K Y+P PEN E Y+ALY  
Sbjct: 486 NIDVLESEQSCALGAAIYAATAAGVYPDVLSAQAAMASNVAKTYQPNPENAEKYQALYQG 545

Query: 544 YAEFGAFVEG 553
           Y   G +V+G
Sbjct: 546 YLALGHYVDG 555


Lambda     K      H
   0.316    0.133    0.398 

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: 881
Number of extensions: 41
Number of successful extensions: 4
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: 562
Length of database: 557
Length adjustment: 36
Effective length of query: 526
Effective length of database: 521
Effective search space:   274046
Effective search space used:   274046
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)

Align candidate 7024890 Shewana3_2064 (ribulokinase (RefSeq))
to HMM TIGR01234 (araB: ribulokinase (EC 2.7.1.16))

# 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/TIGR01234.hmm
# target sequence database:        /tmp/gapView.21612.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01234  [M=536]
Accession:   TIGR01234
Description: L-ribulokinase: ribulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-184  601.0   3.7   1.2e-184  600.9   3.7    1.0  1  lcl|FitnessBrowser__ANA3:7024890  Shewana3_2064 ribulokinase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024890  Shewana3_2064 ribulokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.9   3.7  1.2e-184  1.2e-184       1     531 [.       7     554 ..       7     557 .] 0.95

  Alignments for each domain:
  == domain 1  score: 600.9 bits;  conditional E-value: 1.2e-184
                         TIGR01234   1 ayaiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevldkteaklPadyalqhPadyievleaaikevlaelg 77 
                                       aya+G+d+G++s+ral+vd +tG+e+a+ v  y+r++++ +++ +     +++++qhP dyie+l   ++ + a++ 
  lcl|FitnessBrowser__ANA3:7024890   7 AYALGLDYGSDSVRALLVDTQTGAEVATNVVYYPRWKKGLFCE-P----AKNQFRQHPLDYIESLIEVVQGLWAKAP 78 
                                       79****************************************9.3....369***********************98 PP

                         TIGR01234  78 vdp.advvGiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrinrlaeaeGevflsrygGli 153
                                           + v G+ vd t+st++++d +G +lal+pef+++P+a++ lWkdh+a  ea++i++ a++  e +l+  gG++
  lcl|FitnessBrowser__ANA3:7024890  79 SGAaQRVCGLSVDTTGSTPIAVDESGVALALKPEFENNPNAMFLLWKDHSAIIEAKQITAAANDSSENYLKYEGGIY 155
                                       877578***************************************************************99999*** PP

                         TIGR01234 154 sseWlfakvlqiaeedpeiyeaadrwieaadWivaqlsG.....dlkrsrctaGykalwseskg.yPsasfleelnP 224
                                       sseW++ak l ++++d+e+ +aa +w+e +dWi+a+++G      +k +rc+aG+k +w+es+  yP+++f+  ++P
  lcl|FitnessBrowser__ANA3:7024890 156 SSEWFWAKALFVLRHDAEVRQAAYSWVEHCDWITALMTGtshpkVFKAGRCAAGHKVMWHESWNgYPPNDFFVGIDP 232
                                       ***************************************999988999**************966************ PP

                         TIGR01234 225 slkrivkdkletdigsvgekaGtltekaakllGlpegvvvavgnvdahvsaaaagiaePgklvkiiGtstcdvllge 301
                                        l+  ++dkl  ++ + ++  G lt+++a++lGl   v+v+ g++d+h +a++a+  +Pg l k++Gtstcd+ ++ 
  lcl|FitnessBrowser__ANA3:7024890 233 LLDG-LRDKLPLETCTSDKVCGQLTPEWAQHLGLSTEVIVSFGSFDCHAGAVGAN-VKPGVLTKVMGTSTCDITVAS 307
                                       9986.79************************************************.9******************99 PP

                         TIGR01234 302 kl....ravkGicGvvdggivpGfiGyeaGqsavGdifaWfvkvl............vppelkee.akekqlqllea 361
                                             r +kGicG+vdg+++pG+iG+eaGqsa+Gd +aWf                  +++k + +++ + + l +
  lcl|FitnessBrowser__ANA3:7024890 308 YEdigeRCIKGICGQVDGSVLPGMIGLEAGQSAFGDLYAWFRDLTawpmqqldtsvlFDENIKAKlIQQLESETLTM 384
                                       877899***********************************887789999998766544444443244556667778 PP

                         TIGR01234 362 lsekaakqesgehglvaldWfnGnrsvlvdarlkGvlvgltlatkaeelyralveatafGtrmivetfkesGvavee 438
                                       l ++aak ++ge g+valdW nG+r++ +d+++   ++glt+  +a+++++alvea a+G+r+i+e fk++Gv +++
  lcl|FitnessBrowser__ANA3:7024890 385 LGNAAAKIPVGETGIVALDWINGRRTPDADQSVAMAITGLTMGSQAPQVFKALVEASAYGARAIIERFKQEGVCIDH 461
                                       99*************************************************************************** PP

                         TIGR01234 439 llaaGGiaeknplvmqiyadvlnlplkivasdqapalGaaifaavaageyadipkaaakmgsavektltPisenaar 515
                                       ++++GGi++k +++mq +adv n ++++  s+q++alGaai+aa aag+y d+ +a+a m+s v kt++P++ena++
  lcl|FitnessBrowser__ANA3:7024890 462 VVTIGGISKKSDFIMQTCADVWNCNIDVLESEQSCALGAAIYAATAAGVYPDVLSAQAAMASNVAKTYQPNPENAEK 538
                                       ***************************************************************************** PP

                         TIGR01234 516 yeklyaeykeladyfg 531
                                       y++ly+ y  l +y++
  lcl|FitnessBrowser__ANA3:7024890 539 YQALYQGYLALGHYVD 554
                                       *********9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (557 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.29
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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