GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Aquimarina longa SW024

Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_062061000.1 N456_RS19760 glucosamine-6-phosphate deaminase

Query= reanno::Pedo557:CA265_RS21925
         (641 letters)



>NCBI__GCF_001401755.1:WP_062061000.1
          Length = 639

 Score =  782 bits (2020), Expect = 0.0
 Identities = 374/632 (59%), Positives = 476/632 (75%), Gaps = 6/632 (0%)

Query: 8   EETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVR 67
           E+++FEK+   +F +  IAS  VA+ IA LIK KQ    P VLGLATG +PI VY ELV 
Sbjct: 14  EKSKFEKIHSEIFPDSSIASKLVANEIATLIKQKQQEGNPCVLGLATGSSPIKVYEELVS 73

Query: 68  LHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALE 127
           LH+   LSF NV+TFNLDEYYPM  T  QSY  FM+++LF+HIDI+ +NV+IPDGT+ + 
Sbjct: 74  LHRSGELSFSNVVTFNLDEYYPMDSTHQQSYYHFMHQHLFDHIDINPENVNIPDGTVPIL 133

Query: 128 DIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAAR 187
           ++  +C++YE KI + GGLD Q+LGIGRTGHIGFNEPGS PNSGTR++TLD +TR DA+ 
Sbjct: 134 EMDQYCIDYEMKIKEYGGLDFQLLGIGRTGHIGFNEPGSHPNSGTRIITLDHVTRTDASS 193

Query: 188 DFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSD 247
           DF G   VP KA+TMGI TI K+  ++L+AW  KKASI+K+ +EGE+  ++PA+FLQ   
Sbjct: 194 DFNGLENVPKKAVTMGISTIMKSTRVLLLAWGHKKASIVKETIEGEVISNIPASFLQEHK 253

Query: 248 HVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNG 307
           +   ILD+ AASELTR  TPWLV  C+WT+ L  KAV WL+  L KP+LKLT+ DYN+NG
Sbjct: 254 NTTIILDSEAASELTRIKTPWLVDQCIWTEQLKFKAVTWLSEELTKPVLKLTDKDYNDNG 313

Query: 308 MAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPD 367
           M+ L   +G  YN+NI IFNKLQH+ITGWPGGKPNADD+ RPERA PAKKRV+IFSPHPD
Sbjct: 314 MSSLLAVEGSSYNLNIKIFNKLQHSITGWPGGKPNADDTNRPERALPAKKRVLIFSPHPD 373

Query: 368 DDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGMDNTHLKD 427
           DDVISMGGTFLRL+DQGHDVHV YQTSGN AV D++AL+F E    F    G DN+    
Sbjct: 374 DDVISMGGTFLRLIDQGHDVHVVYQTSGNIAVTDEEALKFAEVANSFQSSNG-DNSS--- 429

Query: 428 LYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGK 487
            Y K+ +F++ K    ID  E++ +KGLIR+ E+I   RY GL DD +HF  LPFYE+GK
Sbjct: 430 -YEKVISFLKSKNQGDIDILEVRQIKGLIRRMESIGATRYFGLNDDKVHFLDLPFYETGK 488

Query: 488 VQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEAWA 547
           ++KNP+ + DI++T  +++K+KP Q+YAAGD  DPHGTH VC + +  ALK L+  E + 
Sbjct: 489 IKKNPLGEEDIKITESIIEKIKPHQIYAAGDLADPHGTHKVCLDAVFSALKNLKPKE-YM 547

Query: 548 QDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFWQ 607
            DCWLW+YRGAW E++  EIEMAVP+SP E+ +K  AI  HQSQKDR +F G+DSREFW 
Sbjct: 548 DDCWLWLYRGAWQEWDVSEIEMAVPLSPDEVSKKTNAILFHQSQKDRVMFQGEDSREFWL 607

Query: 608 RAEDRNRDTAKAYDELGLAEYEAMEAFVRWKF 639
           RA +RNR+TAK YD+LGLA+YEA+EAF ++ F
Sbjct: 608 RARERNRNTAKLYDQLGLADYEAIEAFKKYDF 639


Lambda     K      H
   0.319    0.136    0.412 

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: 1157
Number of extensions: 40
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: 641
Length of database: 639
Length adjustment: 38
Effective length of query: 603
Effective length of database: 601
Effective search space:   362403
Effective search space used:   362403
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: 54 (25.4 bits)

Align candidate WP_062061000.1 N456_RS19760 (glucosamine-6-phosphate deaminase)
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))

# 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/TIGR00502.hmm
# target sequence database:        /tmp/gapView.235527.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00502  [M=259]
Accession:   TIGR00502
Description: nagB: glucosamine-6-phosphate deaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      8e-87  276.8   0.1    1.5e-86  275.9   0.1    1.4  1  NCBI__GCF_001401755.1:WP_062061000.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001401755.1:WP_062061000.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.9   0.1   1.5e-86   1.5e-86      13     248 ..      33     268 ..      25     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: 275.9 bits;  conditional E-value: 1.5e-86
                             TIGR00502  13 sklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglseehPesy 85 
                                           skl a+ ia  i++ k+++ +p vlGlatG++P+++y++l++l+++g++sf++vvtfnldey  +++ h +sy
  NCBI__GCF_001401755.1:WP_062061000.1  33 SKLVANEIATLIKQ-KQQEGNPCVLGLATGSSPIKVYEELVSLHRSGELSFSNVVTFNLDEYYPMDSTHQQSY 104
                                           89999999999*99.888899**************************************************** PP

                             TIGR00502  86 hsfmyenffqhidikpeninilnGnad..dleaecrryeekikslGkidlfllGiGadGhiafnePgsslesr 156
                                           ++fm++++f+hidi+pen+ni++G  +  ++++ c  ye kik++G++d +llGiG+ Ghi+fnePgs  +s 
  NCBI__GCF_001401755.1:WP_062061000.1 105 YHFMHQHLFDHIDINPENVNIPDGTVPilEMDQYCIDYEMKIKEYGGLDFQLLGIGRTGHIGFNEPGSHPNSG 177
                                           *************************994456678*************************************** PP

                             TIGR00502 157 trvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvtisal 229
                                           tr+ tl + t+   s  f+  +++vPkka+t+Gi ti++s +vlll+ G++ka+ vk+ +eg v  ++++s l
  NCBI__GCF_001401755.1:WP_062061000.1 178 TRIITLDHVTRTDASSDFN-GLENVPKKAVTMGISTIMKSTRVLLLAWGHKKASIVKETIEGEVISNIPASFL 249
                                           ************9999998.799************************************************** PP

                             TIGR00502 230 qlhkkvivvadeeaaqelk 248
                                           q hk+ +++ d eaa+el 
  NCBI__GCF_001401755.1:WP_062061000.1 250 QEHKNTTIILDSEAASELT 268
                                           ***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (639 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: 44.27
//
[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:

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