GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella amazonensis SB2B

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 6938546 Sama_2649 beta alanine--pyruvate transaminase (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_08585
         (454 letters)



>FitnessBrowser__SB2B:6938546
          Length = 446

 Score =  296 bits (757), Expect = 1e-84
 Identities = 171/438 (39%), Positives = 245/438 (55%), Gaps = 26/438 (5%)

Query: 13  TLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDEL 72
           T S EH+  PF+  +Q K   PR++ +A+G++  D +GN +LD  AGLWC   G+GR ++
Sbjct: 12  TPSLEHYWMPFTANRQFKAS-PRLLASAEGMFYKDVDGNPVLDSTAGLWCCNAGHGRKKI 70

Query: 73  ADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMV 132
           ++A S Q+REL Y   F Q  HP   ELA  ++DIAP G+N +FFT SGSE  DT L+M 
Sbjct: 71  SEAVSHQIRELDYAPSF-QMGHPLAFELASRLADIAPAGLNRIFFTNSGSESVDTALKMA 129

Query: 133 RHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQ-GDLPIPGIVHIPQPYWFG 191
             Y    GQP +   I R  GYHG    G S+GG+           + G+ H+P      
Sbjct: 130 LAYHRANGQPTRTRFIGRELGYHGVGFGGISVGGIGNNRRTFSQQLLQGVDHLPHTL--- 186

Query: 192 EGGDMTPEEF-------GIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244
              D+    F       G+  A  LE+ I   G + + A I EP+ G+ GVI+PP  Y  
Sbjct: 187 ---DIANNAFSRGFPAHGLEKAEVLEQLITLHGAENIAAVIVEPMSGSAGVILPPQGYLK 243

Query: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVR 304
           R+++I  K+ IL + DEVI GFGR G+ F S  +G+ PD+MT AK L +G IPMG + V 
Sbjct: 244 RLRDITKKHGILLIFDEVITGFGRVGDAFASQRWGVVPDLMTTAKALNNGAIPMGAVFVS 303

Query: 305 DEVVEVLNEGG----DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKR 360
            +V +    G     +F HG+TYSGHPVAAA AL  + I +EEK+ E  + E   Y +  
Sbjct: 304 QDVHDACMTGPEELIEFFHGYTYSGHPVAAAAALATLDIYQEEKLFERTK-ELEGYWEDA 362

Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDT 420
           +  L D P V ++R  GL+  ++L  +     R   +G  +  R  CF NG ++R  GD 
Sbjct: 363 VHSLRDLPNVIDIRNTGLVAGVQLSPNDEGPGR---RGYKVFER--CFRNGTLVRVTGDI 417

Query: 421 MIIAPPLVITKAEIDELV 438
           + ++PPL++ K  ID++V
Sbjct: 418 IAMSPPLIVEKQHIDQIV 435


Lambda     K      H
   0.320    0.140    0.428 

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: 537
Number of extensions: 24
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: 454
Length of database: 446
Length adjustment: 33
Effective length of query: 421
Effective length of database: 413
Effective search space:   173873
Effective search space used:   173873
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: 51 (24.3 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