Alignments for a candidate for gnd in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Shewanella loihica PV-4

Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (characterized)
to candidate 5210117 Shew_2561 6-phosphogluconate dehydrogenase (RefSeq)

Query= CharProtDB::CH_122771
         (517 letters)



>FitnessBrowser__PV4:5210117
          Length = 513

 Score =  437 bits (1124), Expect = e-127
 Identities = 241/504 (47%), Positives = 314/504 (62%), Gaps = 37/504 (7%)

Query: 30  DIGLIGLAVMGQNLILNMADHGYTVVAYNRTTAKVDRFLENEAK------GKSILGAHSI 83
           DIG+IGL VMG+NL LN+AD+ Y V A++  + K D  LE E K       + ILG  ++
Sbjct: 9   DIGVIGLGVMGKNLALNIADNRYRVAAFDLDSTKRDALLEQEQKERPALQAQRILGCSNL 68

Query: 84  KELVDQLKRPRRIMLLVKAGAPVDEFINQLLPY-LEEGDIIIDGGNSHFPDSNRRYEELA 142
            E++  L +PR ++L V AGAPVD   N LL   +E+ DI++D GNS + D+  R  +  
Sbjct: 69  SEMLSSLAKPRVLVLSVPAGAPVDGVCNALLEAGIEQDDIVVDTGNSLWTDTVAREAQYQ 128

Query: 143 KKGILFVGSGVSGGEEGARTGPSLMPGGNEKAWPHIKDIFQDVAAKSD------------ 190
            K I F    +SGGE GAR GPSLMP G+ KAW  IK I++ +AAK D            
Sbjct: 129 DKFIFF-SCAISGGEMGARFGPSLMPSGDIKAWDRIKPIWEAIAAKVDPKTGLPIERQEP 187

Query: 191 ------GEPCCDWVGDAGAGHYVKMVHNGIEYGDMQLICEAYDLMKRVGKFEDKEIGDVF 244
                 GEPC  ++G AGAGHYVKMVHNGIEY DMQLICEAY L+         E+G +F
Sbjct: 188 GNPVTEGEPCTTYIGPAGAGHYVKMVHNGIEYADMQLICEAYQLLSDGLGLSAAEVGKIF 247

Query: 245 ATWNKGVLDSFLIEITRDILYYNDPTDGKPLVEKILDTAGQKGTGKWTAVNALDLGIPVT 304
           A WN+G L+S+L+EI+ D+L   DP  GKPLVE ILD AGQKGTG WTAV++L +G P  
Sbjct: 248 ARWNQGSLNSYLMEISADVLSQADPLTGKPLVEMILDKAGQKGTGLWTAVSSLQIGCPAP 307

Query: 305 LIGEAVFSRCLSAMKAERVEASKALKGPQVTGESPITDKKQFIDDLEQALYASKIISYTQ 364
            I EAV++R +S  K +R + S  L GP+    S   ++  FID+LE ALY +KI  Y Q
Sbjct: 308 TIAEAVYARAVSTQKHQRQQLSLLLAGPEALTLSD-DERAAFIDELENALYCAKIACYAQ 366

Query: 365 GFMLMNQAAKDYGWKLNNAGIALMWRGGCIIRSVFLAEITAAY----RKKPDLENLLLYP 420
           GF LM   A++ GW+L+ A IA +WR GCIIR+ FL  IT AY    R    L+NLL+  
Sbjct: 367 GFQLMAMNAQERGWRLDFAEIAKIWRAGCIIRATFLQSITQAYQQAQRAGESLDNLLMAE 426

Query: 421 FFNDAITKAQSGWRASVGKAIQYGIPTPAFSTALAFYDGLRSERLPANLLQAQRDYFGAH 480
            F+ A++  Q  WR +V +AI  G+P P   +ALA+YD  RSE LPANLLQ QRD+FGAH
Sbjct: 427 TFSLALSAKQQDWRRAVARAIMSGVPVPCIGSALAYYDSYRSETLPANLLQGQRDFFGAH 486

Query: 481 TFKVLPGQENELLKKDEWIHINWT 504
           TF+ +       +   E  H+NW+
Sbjct: 487 TFERID------MPAGEKYHLNWS 504


Lambda     K      H
   0.318    0.137    0.409 

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: 611
Number of extensions: 24
Number of successful extensions: 7
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: 517
Length of database: 513
Length adjustment: 35
Effective length of query: 482
Effective length of database: 478
Effective search space:   230396
Effective search space used:   230396
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: 52 (24.6 bits)

Align candidate 5210117 Shew_2561 (6-phosphogluconate dehydrogenase (RefSeq))
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))

# 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/TIGR00873.hmm
# target sequence database:        /tmp/gapView.444.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00873  [M=467]
Accession:   TIGR00873
Description: gnd: 6-phosphogluconate dehydrogenase (decarboxylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.3e-179  583.8   0.0   1.3e-133  432.2   0.0    2.0  2  lcl|FitnessBrowser__PV4:5210117  Shew_2561 6-phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210117  Shew_2561 6-phosphogluconate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.0   5.4e-48   5.4e-48       1     162 [.       9     176 ..       9     183 .. 0.92
   2 !  432.2   0.0  1.3e-133  1.3e-133     160     466 ..     192     504 ..     185     505 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 5.4e-48
                        TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakg......kklvgaesieefvkslekPrkilllvk 72 
                                      diG+iGl+vmGknl+lniad+ + va+++ +++k d+ll++e+k+      +++ g +++ e+++sl kPr ++l v 
  lcl|FitnessBrowser__PV4:5210117   9 DIGVIGLGVMGKNLALNIADNRYRVAAFDLDSTKRDALLEQEQKErpalqaQRILGCSNLSEMLSSLAKPRVLVLSVP 86 
                                      79*************************************9987652222226899999******************** PP

                        TIGR00873  73 aGaavdavieellpl.lekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayelv 149
                                      aGa+vd v ++ll++ +e+ di++d Gnsl++dt  re + ++k i f    +sGGe Gar+GPslmp G+ +a++ +
  lcl|FitnessBrowser__PV4:5210117  87 AGAPVDGVCNALLEAgIEQDDIVVDTGNSLWTDTVAREAQYQDKFI-FFSCAISGGEMGARFGPSLMPSGDIKAWDRI 163
                                      ***********987559**********************9998866.66899************************** PP

                        TIGR00873 150 epilqkiaakveg 162
                                      +pi ++iaakv+ 
  lcl|FitnessBrowser__PV4:5210117 164 KPIWEAIAAKVDP 176
                                      ***********95 PP

  == domain 2  score: 432.2 bits;  conditional E-value: 1.3e-133
                        TIGR00873 160 vegepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWnegeldsylieitadilkk 237
                                      +egepc++yiG++GaGhyvkmvhnGiey+dmqli+eay+ll ++l+lsa e+ ++f++Wn+g+l+syl+ei+ad+l++
  lcl|FitnessBrowser__PV4:5210117 192 TEGEPCTTYIGPAGAGHYVKMVHNGIEYADMQLICEAYQLLSDGLGLSAAEVGKIFARWNQGSLNSYLMEISADVLSQ 269
                                      689*************************************************************************** PP

                        TIGR00873 238 kded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaaskllsgplaeekae.dkee 313
                                       d   Gkplv++ild+agqkGtG Wta+++l+ G P  +i+e+v+ar++s++k++r + s ll+gp+a + +  ++++
  lcl|FitnessBrowser__PV4:5210117 270 ADPLtGKPLVEMILDKAGQKGTGLWTAVSSLQIGCPAPTIAEAVYARAVSTQKHQRQQLSLLLAGPEALTLSDdERAA 347
                                      **977************************************************************988776553899* PP

                        TIGR00873 314 fiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkikkafeenp....elenllla 387
                                      fi+++++aly++ki +yaqGf+l+++ ++e+gw l+++eia+iwr+Gciir++fl++i++a+++ +    +l nll+a
  lcl|FitnessBrowser__PV4:5210117 348 FIDELENALYCAKIACYAQGFQLMAMNAQERGWRLDFAEIAKIWRAGCIIRATFLQSITQAYQQAQrageSLDNLLMA 425
                                      **************************************************************98652222689***** PP

                        TIGR00873 388 eyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteW 465
                                      e f  al+++q+++r++va+ai +g+pvP++ +al++yd+yr+++lpanllq+qrd+fGaht+er+d+p ge++h +W
  lcl|FitnessBrowser__PV4:5210117 426 ETFSLALSAKQQDWRRAVARAIMSGVPVPCIGSALAYYDSYRSETLPANLLQGQRDFFGAHTFERIDMPAGEKYHLNW 503
                                      ****************************************************************************** PP

                        TIGR00873 466 l 466
                                      +
  lcl|FitnessBrowser__PV4:5210117 504 S 504
                                      8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (513 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: 14.14
//
[ok]

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

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Protein sequences (fasta format)
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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