Alignments for a candidate for gnd in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Shewanella sp. ANA-3

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate 7024499 Shewana3_1677 6-phosphogluconate dehydrogenase (RefSeq)

Query= BRENDA::P80859
         (469 letters)



>FitnessBrowser__ANA3:7024499
          Length = 508

 Score =  429 bits (1103), Expect = e-124
 Identities = 237/490 (48%), Positives = 304/490 (62%), Gaps = 29/490 (5%)

Query: 6   IGVIGLAVMGKNLALNIESRGFSVSVYNRSSSKTEEFLQEAKGKNV------VGTYSIEE 59
           IGVIGL VMGKNLALNI    + VS ++    K    LQ+ K + V       G  ++ E
Sbjct: 10  IGVIGLGVMGKNLALNIADNQYRVSAFDLDPVKVNGVLQQEKQERVGQELRITGCANLSE 69

Query: 60  FVQSLETPRKILLMVKAGTATDATIQSLLPH-LEKDDILIDGGNTYYKDTQRRNKELAES 118
            + SL  PR ++L V AG   D    +L+   +E DDI+ID GN+ + DT  R K     
Sbjct: 70  MLASLAHPRILVLSVPAGAPVDGVCHALISAGIEADDIVIDTGNSLWTDTVEREKRYQGK 129

Query: 119 GIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVKPILEAISAKVD-------------- 164
            I F  + VSGGE GA  GPS+MP G   A + V PI +AI+AKVD              
Sbjct: 130 FI-FFSSAVSGGEVGARFGPSLMPSGDLGAWQNVAPIWKAIAAKVDPQTGLPIERFEPGN 188

Query: 165 ----GEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLISESYFILKQVLGLSADELHEVFAE 220
               GEPCTTYIGP GAGHYVKMVHNGIEY DMQLI E+Y ++   LG+SA ++ EVF  
Sbjct: 189 PVTDGEPCTTYIGPAGAGHYVKMVHNGIEYADMQLICEAYQLMLDGLGMSAAQVGEVFER 248

Query: 221 WNKGELDSYLIEITADIFTKKDEETGKPLVDVILDKAGQKGTGKWTSQSALDLGVPLPII 280
           WNKG L+SYL+ I+A++  + D  TG+PLV++ILDKAGQKGTG WT+ S+L +G P P I
Sbjct: 249 WNKGSLNSYLMGISAEVLKQADPLTGQPLVEMILDKAGQKGTGLWTAVSSLQIGCPAPTI 308

Query: 281 TESVFARFISAMKEERVKASGLLSGP-EVKPVTENKEELIEAVRKALFMSKICSYAQGFA 339
            E+V+AR +S  K  RV+ S  L+GP  V      K  LI+A+  AL+ +K+C YAQGF 
Sbjct: 309 AEAVYARAVSTQKSLRVELSKKLAGPASVAMDDAQKASLIDALESALYCAKVCCYAQGFQ 368

Query: 340 QMKAASEEYNWDLKYGEIAMIFRGGCIIRAAFLQKIKEAYDREPELDNLLLDSYFKNIVE 399
            M   ++E  W L + EIA I+R GCIIRA FLQ I +AY  + +L  LL+   F   + 
Sbjct: 369 LMAMTAQEQKWQLDFAEIAKIWRAGCIIRATFLQSITQAYQADADLSCLLMADIFATTLS 428

Query: 400 SYQGALRQVISLAVAQGVPVPSFSSALAYYDSYRTAVLPANLIQAQRDYFGAHTYERTDK 459
             Q   R  ++ AV QG+PVP  SSALAYYDSYR+  LPANL+Q QRD+FGAHT+ER DK
Sbjct: 429 EKQTEWRSAVAAAVMQGIPVPCISSALAYYDSYRSETLPANLLQGQRDFFGAHTFERLDK 488

Query: 460 EG--IFHTEW 467
                +H +W
Sbjct: 489 PAGEKYHLDW 498


Lambda     K      H
   0.315    0.134    0.379 

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: 571
Number of extensions: 22
Number of successful extensions: 5
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: 469
Length of database: 508
Length adjustment: 34
Effective length of query: 435
Effective length of database: 474
Effective search space:   206190
Effective search space used:   206190
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 (21.5 bits)
S2: 52 (24.6 bits)

Align candidate 7024499 Shewana3_1677 (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.32680.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.9e-180  586.0   0.2   8.8e-179  581.1   0.2    2.0  1  lcl|FitnessBrowser__ANA3:7024499  Shewana3_1677 6-phosphogluconate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024499  Shewana3_1677 6-phosphogluconate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.1   0.2  8.8e-179  8.8e-179       1     466 [.       9     499 ..       9     500 .. 0.94

  Alignments for each domain:
  == domain 1  score: 581.1 bits;  conditional E-value: 8.8e-179
                         TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgk.....klvgaesieefvkslekPrkilllvk 72 
                                       diG+iGl+vmGknl+lniad+ + v++++ ++ k++ +l++e++++     +++g  ++ e+++sl +Pr ++l v 
  lcl|FitnessBrowser__ANA3:7024499   9 DIGVIGLGVMGKNLALNIADNQYRVSAFDLDPVKVNGVLQQEKQERvgqelRITGCANLSEMLASLAHPRILVLSVP 85 
                                       79*************************************998765433333799*********************** PP

                         TIGR00873  73 aGaavdavieellpl.lekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayel 148
                                       aGa+vd v ++l+ + +e  di+id Gnsl++dt  rek  + k i f  + vsGGe Gar+GPslmp G+  a+++
  lcl|FitnessBrowser__ANA3:7024499  86 AGAPVDGVCHALISAgIEADDIVIDTGNSLWTDTVEREKRYQGKFI-FFSSAVSGGEVGARFGPSLMPSGDLGAWQN 161
                                       **********9986549**********************9998866.67899************************* PP

                         TIGR00873 149 vepilqkiaakv..................egepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealkls 207
                                       v+pi ++iaakv                  +gepc++yiG++GaGhyvkmvhnGiey+dmqli+eay+l+ ++l++s
  lcl|FitnessBrowser__ANA3:7024499 162 VAPIWKAIAAKVdpqtglpierfepgnpvtDGEPCTTYIGPAGAGHYVKMVHNGIEYADMQLICEAYQLMLDGLGMS 238
                                       **********973333333333333332224689******************************************* PP

                         TIGR00873 208 aeeiaevfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfar 283
                                       a ++ evfe+Wn+g+l+syl+ i+a++lk+ d   G+plv++ild+agqkGtG Wta+++l+ G P  +i+e+v+ar
  lcl|FitnessBrowser__ANA3:7024499 239 AAQVGEVFERWNKGSLNSYLMGISAEVLKQADPLtGQPLVEMILDKAGQKGTGLWTAVSSLQIGCPAPTIAEAVYAR 315
                                       ********************************977****************************************** PP

                         TIGR00873 284 vlsslkeervaaskllsgplaeekae.dkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrg 359
                                       ++s++k+ rv+ sk+l+gp ++ +   +k+++i+++++aly++k+++yaqGf+l++++++e  w+l+++eia+iwr+
  lcl|FitnessBrowser__ANA3:7024499 316 AVSTQKSLRVELSKKLAGPASVAMDDaQKASLIDALESALYCAKVCCYAQGFQLMAMTAQEQKWQLDFAEIAKIWRA 392
                                       ******************877665443999*********************************************** PP

                         TIGR00873 360 GciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpan 436
                                       Gciir++fl++i++a++++ +l+ ll+a+ f+ +l+++q+++r++va a+ +gipvP++s+al++yd+yr+++lpan
  lcl|FitnessBrowser__ANA3:7024499 393 GCIIRATFLQSITQAYQADADLSCLLMADIFATTLSEKQTEWRSAVAAAVMQGIPVPCISSALAYYDSYRSETLPAN 469
                                       ***************************************************************************** PP

                         TIGR00873 437 llqaqrdyfGahtyertdkprgeffhteWl 466
                                       llq+qrd+fGaht+er dkp ge++h +W+
  lcl|FitnessBrowser__ANA3:7024499 470 LLQGQRDFFGAHTFERLDKPAGEKYHLDWS 499
                                       *****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (508 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 2.81
//
[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