GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Herbaspirillum seropedicae SmR1

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate HSERO_RS00450 HSERO_RS00450 phosphoenolpyruvate-protein phosphotransferase

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



>FitnessBrowser__HerbieS:HSERO_RS00450
          Length = 595

 Score =  303 bits (775), Expect = 3e-86
 Identities = 200/564 (35%), Positives = 299/564 (53%), Gaps = 26/564 (4%)

Query: 404 AGDQVNGIAASPGIAIGPVLVRKPQVID---YPKRGESPVIELQRLDAALDKVHADIGTL 460
           A   ++GIA S GIAIG   +  P  +D   Y    +    E++RL +A+  VH ++ T+
Sbjct: 2   ASFSLHGIAVSQGIAIGRAHLMAPAALDVKHYLIAADQVEAEIERLKSAVKAVHQELHTI 61

Query: 461 IDE---SQVASIRDIFTTHQAMLKDPALREEVQ-VRLQKGLSAEAAWMEEIESAAQQQEA 516
             E        +      H  +L DP L E  Q +   +  +AE A + +IE  + Q + 
Sbjct: 62  RSELPREAPPELGAFIDVHSLILSDPMLAEVPQDIIRHRYYNAEWALVTQIEELSAQFDE 121

Query: 517 LHDKLLAERAADLRDVGRRVLACLTGVEAEQAPDEP----YILVMDEVAPSDVATLNAQR 572
           + D  L ER AD++ VG R+L  LTG      P        I+V  +++P+D+       
Sbjct: 122 IEDPYLRERKADIQQVGERILKVLTGSATHLPPSGEAAANIIIVAHDISPADMLQFREST 181

Query: 573 VAGILTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQ 632
            AG +T  GG  SH+AI+AR+L IPA VG     + +  + +L++DG+ G ++V PS   
Sbjct: 182 FAGFVTDLGGPNSHTAIVARSLAIPAAVGMHNASVLVKHDDVLIIDGDAGVVIVDPSPLV 241

Query: 633 LEQ--ARSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIG 690
           L Q  AR ER  RE +K   +  +   A+T+DG P+ + ANI   G+   A   GA GIG
Sbjct: 242 LAQYRARQERLLRERKK--LSRLKKTPAITQDGEPITLLANIELPGDAVTAFEAGAMGIG 299

Query: 691 LLRTELVFMNHS----QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPA 746
           L R+E +FM  +    + P++  Q   Y++ + A++GR + +RTLDVG DKPL      A
Sbjct: 300 LFRSEFLFMGRAGHLEKFPSEDEQFEHYKQAVIAMKGRSVTIRTLDVGADKPLDEDEETA 359

Query: 747 EENPFLGVRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRL 806
             NP LG+R IR  L  P +  TQLRA+L ++   P++++ PM+ +  E     AM+D+ 
Sbjct: 360 L-NPALGLRAIRYCLSEPQMFLTQLRAILRASAFGPIKLLVPMMAHAFEIDQTLAMIDQA 418

Query: 807 RVELPVA------DLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPT 860
           + +L         ++ VG MIEIP+AAL  P+  + +DF SIGTNDL QYTLAIDR    
Sbjct: 419 KQQLRERKQKFDEEIPVGAMIEIPAAALALPLFVKRLDFLSIGTNDLIQYTLAIDRVDHE 478

Query: 861 LSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARS 920
           ++   D LHPAVL L+   +      G  V VCGE+A D     LL+G+G+ E S+    
Sbjct: 479 VAHLYDPLHPAVLFLLSTVISQGRKAGIPVSVCGEMAGDLKWTRLLLGMGLLEFSMHPSQ 538

Query: 921 IALVKARVRELDFAACQRLAQQAL 944
           I  VK  +   D    +   ++ L
Sbjct: 539 ILSVKNEILNSDLRLLEPQVKKVL 562


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: 1160
Number of extensions: 55
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: 960
Length of database: 595
Length adjustment: 40
Effective length of query: 920
Effective length of database: 555
Effective search space:   510600
Effective search space used:   510600
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