GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas simiae WCS417

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate GFF827 PS417_04200 aldehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__WCS417:GFF827
          Length = 481

 Score =  268 bits (685), Expect = 3e-76
 Identities = 166/466 (35%), Positives = 245/466 (52%), Gaps = 20/466 (4%)

Query: 41  INGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAV 100
           ING+ V      V++NP++  +V+G  +KA       AI AA  AF  W  +  + R   
Sbjct: 11  INGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARHDA 70

Query: 101 LFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSR 160
           L +  +++  R+ E   LL +E GK   EA  +   A +  +++A + + L+     + R
Sbjct: 71  LDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPSVR 130

Query: 161 EGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEV 220
            G   +      GV  +I PWNF  AI A      +  GN VV+KPA   P  A    E+
Sbjct: 131 PGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALAEI 190

Query: 221 LEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRI----FERAAKVQPG 276
           +  +G P GV N V GSG  VGD LV+ PK   I+FTGS  VG +I      R AKVQ  
Sbjct: 191 ISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ-- 248

Query: 277 QQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQV 336
                    EMGGK+  ++ +DAD++ A +    SAF   GQ+C+A SR +V   ++DQ 
Sbjct: 249 --------LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQF 300

Query: 337 LERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--TGDDS 393
           +  + E  +S        +   +GPV+ Q   D+ + YI+IG+ EG RLVSGG     D+
Sbjct: 301 VAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDT 360

Query: 394 KGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNR 453
           +GY++ PT+FAD +   R+ +EEIFGPV    +V+D++ AL +AN+TE+GL+  + T + 
Sbjct: 361 EGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL 420

Query: 454 KHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGG 498
           K+    K+    G +  N    G  V YH PFGG K S   S+  G
Sbjct: 421 KYANHFKRHSQAGMVMVNLPTAG--VDYHVPFGGRKGSSYGSREQG 464


Lambda     K      H
   0.316    0.133    0.379 

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: 564
Number of extensions: 25
Number of successful extensions: 3
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: 515
Length of database: 481
Length adjustment: 34
Effective length of query: 481
Effective length of database: 447
Effective search space:   215007
Effective search space used:   215007
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 (21.6 bits)
S2: 52 (24.6 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