GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Herbaspirillum seropedicae SmR1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS17580 HSERO_RS17580
           hypothetical protein
          Length = 440

 Score =  197 bits (500), Expect = 7e-55
 Identities = 137/415 (33%), Positives = 204/415 (49%), Gaps = 49/415 (11%)

Query: 26  VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHTGNGYTNEPV 83
           V GEG  L DQ GK YID +GG AV+ LGH HPR+++A+ +Q G+  + HT + +T  P 
Sbjct: 17  VAGEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHT-SFFTTAPA 75

Query: 84  LRLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141
             LA  L DA     + V+F + G+EA EAALKLAR+Y  +    ++  I+A + ++HG 
Sbjct: 76  EELAAMLADAAPGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRRHIIARRQSYHGN 135

Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHAI-----------YNDLDSAKALID--------- 181
           TL  ++ GG     + F P+  +  H              +D+   + L D         
Sbjct: 136 TLGALAIGGNAWRREMFMPMLIEAHHVSPCYAYRNRADGESDVQYVQRLADELEQKILSL 195

Query: 182 --DNTCAVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAY 238
             D   A + E + G   G VP   D+ R +R +CD +  LLI DEV +G+GRTG L+A 
Sbjct: 196 GADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGRTGYLFAC 255

Query: 239 MHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGGNPLACAVAG 293
              GV PD++  AK LG G+ PIGA++ S+     +  G+    HG TY G+  ACA A 
Sbjct: 256 EEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHTYIGHATACAAAV 315

Query: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKA-- 351
            V  TI    +L  V+QR +     L           +IRG GL +G  L  E + K   
Sbjct: 316 AVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVELVAERSSKLPL 375

Query: 352 -------KAISNQAAEEGLMILIAGANV-------VRFAPALIISEDEVNSGLDR 392
                    +  +A + GL++   G  +       +  AP  I S ++++  + R
Sbjct: 376 SPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSNDISEIVQR 430


Lambda     K      H
   0.321    0.137    0.412 

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: 434
Number of extensions: 28
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: 406
Length of database: 440
Length adjustment: 32
Effective length of query: 374
Effective length of database: 408
Effective search space:   152592
Effective search space used:   152592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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