Aligments for a candidate for fruI in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruI in Shewanella amazonensis SB2B

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 6937494 Sama_1650 phosphotransferase system, enzyme I (RefSeq)

Query= reanno::psRCH2:GFF3291
         (960 letters)



>FitnessBrowser__SB2B:6937494
          Length = 567

 Score =  355 bits (911), Expect = e-102
 Identities = 219/574 (38%), Positives = 322/574 (56%), Gaps = 30/574 (5%)

Query: 407 QVNGIAASPGIAIGPVLV----RKPQVIDYPKRGESPVIE-LQRLDAALDKVHADIGTLI 461
           QVNGIA  PG+  G  L      KP  +DY       + + L RLD  L ++   +   +
Sbjct: 2   QVNGIAIKPGVTFGEALHFNTGHKP--LDYRILPIKRIPQQLSRLDGGLARLKQQLSASL 59

Query: 462 DESQVASIRDIFTTHQA---MLKDPALREEV-----QVRLQKGLSAEAAWMEEIESAAQQ 513
                 S  D +   +A    L DP LR  +     Q++    +S E  +  +    A +
Sbjct: 60  QALDSQS--DAYALVEADLLYLDDPDLRAHIADTITQLQFSACVSIERVFAHQ----ASE 113

Query: 514 QEALHDKLLAERAADLRDVGRRVLACLTGVEAEQAPDE---PYILVMDEVAPSDVATLNA 570
            EAL D  LA+RA D+R +G+R++  + G    Q P +   P IL+ D+++P++ A L  
Sbjct: 114 LEALDDPYLAQRAEDVRSLGKRLIQAVFG-HPGQEPGKLKVPTILLADDISPAEFAVLPL 172

Query: 571 QRVAGILTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSG 630
           + VAGI+   GG TSH+AI+ARA GIPA++      LG+     L +DG+ G L   P G
Sbjct: 173 ENVAGIVLKSGGLTSHTAILARAAGIPALLSCPYSELGINNGDQLAIDGDAGALYRNPEG 232

Query: 631 AQLEQARSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIG 690
             LE  R   A+    +   ++ R   A+T+DGH + + AN+G   +  +   +GA+GIG
Sbjct: 233 GTLELLRQHEASARLAREQLDQYRDKPAMTQDGHEISLLANVGNLNDVLKVSGLGADGIG 292

Query: 691 LLRTELVFMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENP 750
           LLRTE + M+ +  P++  Q   Y   + ALEGR L +RTLD+G DK LP      EENP
Sbjct: 293 LLRTEFMLMHSATLPDERAQYQLYSDAIHALEGRVLTIRTLDIGADKELPCLCQVKEENP 352

Query: 751 FLGVRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVEL 810
            LG+RGIR +L  P +L+TQLRA+L +A+   +R+MFPMV  ++E     A+++  R EL
Sbjct: 353 ALGLRGIRYTLANPQLLKTQLRAVLRAANHGHVRLMFPMVNQVEELDAVLALLETCRREL 412

Query: 811 P-----VADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQA 865
                   D+ +GI++E P+A L  P +   +DF SIGTNDLTQY +A DRG+P L+   
Sbjct: 413 DDEEKGFGDISLGIVVETPAAVLNLPAMLPMLDFVSIGTNDLTQYAMAADRGNPCLARDY 472

Query: 866 DGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVK 925
             L PAVLRLI MT+++A +    V +CGE+ +D   VPLL+GLG DELSV+  ++  VK
Sbjct: 473 PALSPAVLRLISMTLQSARSQDVKVSLCGEMGSDPRLVPLLIGLGFDELSVNVGAMLEVK 532

Query: 926 ARVRELDFAACQRLAQQALMLPGAHEVRAFVGEH 959
           A +   +F  C +LA +ALM     E+ A +  +
Sbjct: 533 AAICRQEFDRCTQLAGRALMADRLSELDACISSY 566


Lambda     K      H
   0.317    0.134    0.384 

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: 1065
Number of extensions: 38
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: 960
Length of database: 567
Length adjustment: 40
Effective length of query: 920
Effective length of database: 527
Effective search space:   484840
Effective search space used:   484840
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: 55 (25.8 bits)

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)
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