GapMind for catabolism of small carbon sources

 

Alignments 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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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